Compositions for improving cells and organisms

ABSTRACT

The present invention provides compositions comprising randomized in-frame fusion polynucleotides and methods for introducing them into a host organism to obtain desirable phenotypic changes that modulate tolerance to stress, thus creating novel characteristics of the transformed organism.

This application is the National Phase Under 35 U.S.C. § 371 of PCT International Application No. PCT/US15/43285 filed on Jul. 31, 2015, which claims priority under 35 U.S.C. § 119(e) on U.S. Provisional Application No. 62/031,624 filed on Jul. 31, 2014, the entire contents of each of which are hereby incorporated by reference.

FIELD OF THE INVENTION

This invention relates to non-naturally occurring fusion polynucleotides encoding fusion polypeptides and methods of introducing the fusion polynucleotides into host organisms to generate new and/or improved phenotypes.

BACKGROUND OF THE INVENTION

Currently, there is a shift to biological systems for production of a variety of chemicals and fuels, and a wide assortment of organisms are and will be used, most of them microbes, with an increasing tendency towards photosynthetic organisms (Dismukes 2008). The ability to grow robustly, the ability to resist toxic compounds, abiotic stresses, changes in growth conditions, and efficient production of the materials and compounds of interest, are desirable properties of these organisms.

Yeasts are widely employed as fermentation organisms for the production of ethanol, butanol, isobutanol and other alcohols, and a variety of commodity and fine chemicals. Yeasts used for bio-production include the baker's yeast Saccharomyces cerevisiae; other Saccharomyces species; Schizosaccharomyces pombe; Kluyveromyces species such as K. lactis, K. marxianus and K. thermotolerans; Candida species such as C. albicans, C. glabrata, C. stellate, C. tropicalis, C. dubliniensis and C. keroseneae; Pichia species such as P. angusta, P. anomala, P. membranifaciens and P. pastoris; oleaginous yeasts such as Yarrowia lipolytica; and other yeast species such as Dekkera/Brettanomyces species, Brettanomyces bruxellensis, Torulaspora delbrueckii and Zygosaccharomyces bailii.

Many biological production systems using S. cerevisiae and other eukaryotic and prokaryotic production hosts depend on resistance and tolerance properties of the production organisms for efficient production of the desired chemical. For example, many fermentation processes are exothermic and require the removal of heat or cooling of bioreactors to ensure the continued viability and productivity of the organism used for fermentation. Media used for production can have low or high pH values (i.e. pH<5.0 for low pH values, pH>9.0 for high pH values) due to acidic or basic pre-treatment processes that were used for the production of sugars used in the fermentation. Alternatively, media used in fermentation can contain salts (i.e. sodium chloride) resulting from neutralization with bases or acids of the acids and bases used in the pre-treatment processes. Because the growth of many species of microbes, including many yeasts, is inhibited by heat, salt, low pH or high pH, it is often necessary to employ microbes that are naturally tolerant or resistant to these abiotic stresses, or to engineer sensitive strains and species of microbes for higher levels of tolerance or resistance.

Alcohols, such as ethanol, butanol and isobutanol are common products of fermentation processes employing yeasts and other microbes. Alcohols are toxic compounds and can be tolerated by yeasts and other microbes only in limited concentrations. Although some ethanol-producing yeast species are naturally resistant to ethanol (for example Saccharomyces cerevisiae), higher ethanol tolerance is generally desirable in ethanol-producing industrial yeast strains to maximize the productivity of fermentation processes. Other alcohols such as butanol are highly toxic at low concentrations, and yeast species that are naturally resistant to these alcohols have not been found. It is therefore broadly desirable to enhance alcohol tolerance in yeast species used for the production of alcohols (Cakar 2012, Doğan 2014).

Furthermore, the feedstocks used in a variety of biological production systems, particularly those feedstocks derived from degradation of plant products, often contain elevated concentrations of salts, acetate, growth-inhibitory carbohydrates, or various toxic organic compounds derived from plant lignins. The ability of a production organism to tolerate the presence of these toxic compounds is a prerequisite for maximal productivities. In addition, the pH found in production systems may be outside the pH optimum for the production organism used, and the organism's ability to grow at pH values outside of its natural optimum may be important in certain production systems.

Renewable biomass, including lignocellulosic material and agricultural residues such as corn fiber, corn stover, corn cob, wheat straw, rice straw, and sugarcane bagasse, are low cost materials for bioethanol production. Dilute acid hydrolysis is commonly used in biomass degradation which hydrolyzes cellulose and hemicellulose fractions to increase fiber porosity to allow enzymatic saccharification and fermentation of the cellulose fraction. (Saha 2003). However, acid hydrolysis both acidifies the resulting mix of sugars and also generates inhibitory compounds that interfere with microbial growth and hinders subsequent fermentation. These compounds include aldehydes (such as furfural, 5-hydroxymethylfurfural, etc.), ketones, phenols, and organic acids (such as acetic, formic, levulinic acids, etc.). Two of the most potent inhibitors are furfural and 5-hydroxymethylfurfrual (5-hydroxymethylfurfrual referred to as “HMF” hereafter). Yeast growth can be reduced by the combination of furfural and HMF at concentrations as low as 5 mM (Liu 2004).

These inhibitors can be removed from the hydrolysate before its use in fermentation, using physical chemical or enzymatic steps and treatments. However, these additional steps add complexity to the production process, produce waste products, and add significantly to the production cost. Alternatively, species or strains of microbes or yeasts need to be used for fermentation that are resistant to inhibitors present in sugars derived from biomass and other sources, resistant to ethanol and other products of the fermentation, and/or tolerant of abiotic stresses such as high temperature, high salt and low pH that are frequently encountered during fermentation processes (Cakar 2012, Doğan 2014). Most yeast strains, including industrial strains, are susceptible to the growth-inhibiting compounds released by dilute acid hydrolysis pre-treatment (Martin 2003). Yet few yeast strains tolerant to inhibitors are available and the need for tolerant strains is well recognized (Klinke 2004, Zaldivar 2001, Nieves 2015).

Genetic or epigenetic changes in organisms can improve the organisms' performance and raise their productivities. Particularly useful is the introduction of nucleic acids that confer dominant traits. This implies that the functions performed by the introduced nucleic acids, whether they encode RNA or protein or perform another function in the cell or organism, alter or overrides the function performed by similar nucleic acids that are naturally present in the cell or organism.

The present disclosure describes 83 fusion polynucleotides that confer resistance and tolerance in S. cerevisiae to alcohols and to abiotic stresses such as heat, salt, and low pH. These fusion polynucleotides are generated by pairwise fusion of full length open reading frames present in the S. cerevisiae genome. They are useful for improving S. cerevisiae, other yeasts, and other production microbes and to raise the productivity of a variety of biological production systems.

BRIEF SUMMARY OF THE INVENTION

The fusion polynucleotides described in the present disclosure were isolated from fusion polynucleotide libraries prepared by fusing pairs of intact S. cerevisiae open reading frames precisely and in-frame in a random manner, inserting the pairwise gene fusions into a plasmid vector containing sequences for their propagation in bacteria and in yeast, expressing the fusion polynucleotides in yeast, generating a population of yeast cells harboring these fusion gene constructs, selecting the population for resistance to a variety of products and stresses, including ethanol, butanol, heat, salt and low pH, and recovering the plasmids from cells surviving the selections as set forth in U.S. Ser. No. 14/134,619. The plasmids were then individually tested for their ability to confer alcohol or stress tolerance in yeast. Of the 83 fusion polynucleotides described in the present disclosure, 63 were isolated and tested in this manner (SEQ ID NO: 1-63). Twenty additional fusion polynucleotides (SEQ ID NO: 205-224) were prepared individually and in a targeted manner by combining open reading frames identified among the first 63 fusion polynucleotides with each other, or with additional open reading frames present in the yeast genome, in new sequence combinations.

Among the fusion polynucleotides listed in the disclosure are multiple ones (61 different fusion polynucleotides) containing the yeast WHI2 gene (Saul 1985, Mountain 1990, Mountain 1990a, Radcliffe 1997, Kaida 2002, Leadsham 2009, Mendl 2011, Müller 2011). WHI2 has previously been implicated in stress tolerance (Mendl 2011, Willer 2011) as well as a variety of other cellular processes, including regulation of colony morphology, control of cell division and cell size, nutritional sensing, and mitochondrial function.

Among the fusion polynucleotides listed in the disclosure are two fusion polynucleotides and their corresponding fusion proteins which represent fusions of the WHI2 protein with phosphatases, 14 fusion polynucleotides and their corresponding fusion proteins which represent fusions of the WHI2 protein with members of the KEOPS complex, a conserved protein complex with a role in telomere maintenance, but of largely unknown function (Bianchi 2006, Downey 2006), as well as 11 fusion polynucleotides and their corresponding fusion proteins which represent fusions of the WHI2 protein with members of the EGO complex, a vacuolar membrane-associated protein complex with a role in activation of microautophagy during exit from rapamycin-induced growth arrest (Dubouloz 2005, Gao 2006, Piper 2006).

The present disclosure describes the sequences of these 83 fusion polynucleotides, and their activity for conferring stress and alcohol tolerance.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIG. 1—Table 5A: Heat and ethanol resistance and tolerance activities of 19 fusion polynucleotides and their individual constituent ORFs in glucose-containing medium in S. cerevisiae.

FIG. 2—Table 5B: Butanol and low pH resistance and tolerance activities of 19 fusion polynucleotides and their individual constituent ORFs in glucose-containing medium in S. cerevisiae.

FIG. 3—Table 6A: Heat and ethanol resistance and tolerance activities of 20 KEOPS/EGO fusion polynucleotides and their individual constituent ORFs in glucose-containing medium in S. cerevisiae.

FIG. 4—Table 6B: Butanol and low pH resistance and tolerance activities of 20 KEOPS/EGO fusion polynucleotides and their individual constituent ORFs in glucose-containing medium in S. cerevisiae.

FIG. 5—Table 7A: Heat, ethanol, butanol, low pH and salt resistance and tolerance activities of 6 fusion polynucleotide GAL1 centromeric plasmids and their corresponding individual ORF GAL1 centromeric plasmids in galactose-containing medium in S. cerevisiae.

FIG. 6—Table 7B: Heat, ethanol, butanol, low pH and salt resistance and tolerance activities of 9 fusion polynucleotide GAL1 centromeric plasmids and their corresponding individual ORF GAL1 centromeric plasmids in galactose-containing medium in S. cerevisiae.

DETAILED DESCRIPTION OF THE INVENTION

The following abbreviations and definitions will be used for the interpretation of the specification and the claims.

As used herein, the terms “comprises,” “comprising,” “includes,” “including,” “has,” “having,” “contains” or “containing,” or any other variation thereof, are intended to cover a non-exclusive inclusion. For example, a composition, a mixture, process, method, article, or apparatus that comprises a list of elements is not necessarily limited to only those elements but may include other elements not expressly listed or inherent to such composition, mixture, process, method, article, or apparatus. Further, unless expressly stated to the contrary, “or” refers to an inclusive or and not to an exclusive or. For example, a condition A or B is satisfied by any one of the following: A is true (or present) and B is false (or not present), A is false (or not present) and B is true (or present), and both A and B are true (or present).

Complementary nucleotide sequence: As used herein, a complementary nucleotide sequence is a sequence in a polynucleotide chain in which all of the bases are able to form base pairs with a sequence of bases in another polynucleotide chain.

Composite open reading frame: As used herein, a composite open reading frame results from the in-frame fusion of at least two different starting open reading frames, resulting in a new open reading frame comprising all starting open reading frames and encoding a fusion protein comprising the sequences encoded by all starting open reading frames

Control elements: The term ‘control elements’ refers to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing site, effector binding site and stem-loop structure.

Degenerate Sequence: In this application degenerate sequences are defined as populations of sequences where specific sequence positions differ between different molecules or clones in the population. The sequence differences may be a single nucleotide or multiple nucleotides of any number, examples being 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900 or 1000 nucleotides, or any number in between. Sequence differences in a degenerate sequence may involve the presence of 2, 3 or 4 different nucleotides in that position within the population of sequences, molecules or clones. Examples of degenerate nucleotides in a specific position of a sequence are: A or C; A or G; A or T; C or G; C or T; G or T; A, C or G; A, C or T; A, G or T; C, G or T; A, C, G or T.

Discrete Random Polynucleotide: A discrete random polynucleotide refers to a specific polynucleotide within a mixed collection of polynucleotides, chosen randomly from the collection.

Expression: The term “expression”, as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid disclosed, as well as the accumulation of polypeptide as a product of translation of mRNA.

Full-length Open Reading Frame: As used herein, a full-length open reading frame refers to an open reading frame encoding a full-length protein which extends from its natural initiation codon to its natural final amino-acid coding codon, as expressed in a cell or organism. In cases where a particular open reading frame sequence gives rise to multiple distinct full-length proteins expressed within a cell or an organism, each open reading frame within this sequence, encoding one of the multiple distinct proteins, can be considered full-length. A full-length open reading frame can be continuous or may be interrupted by introns.

Fusion polynucleotide: A fusion polynucleotide as used in this application refers to a polynucleotide that results from the operable joining of two separate and distinct polynucleotides into a single polynucleotide. In the context of this application, the term in-frame fusion polynucleotide is defined as a fusion polynucleotide encoding a fusion polypeptide.

Fusion polypeptide: A fusion polypeptide is an expression product resulting from the fusion of two or more open reading frames that originally coded for separate proteins.

Gene: The term “gene” refers to a nucleic acid fragment that is capable of being expressed as a specific protein, optionally including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature in its natural host organism. “Natural gene” refers to a gene complete with its natural control sequences such as a promoter and terminator. “Chimeric gene” refers to any gene that comprises regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. Similarly, a “foreign” gene refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. A “transgene” is a gene that has been introduced into the genome by a transformation procedure.

In-Frame: The term “in-frame” in this application, and particularly in the phrase “in-frame fusion polynucleotide,” refers to the reading frame of codons in an upstream or 5′ polynucleotide or ORF as being the same as the reading frame of codons in a polynucleotide or ORF placed downstream or 3′ of the upstream polynucleotide or ORF that is fused with the upstream or 5′ polynucleotide or ORF. Such in-frame fusion polynucleotides typically encode a fusion protein or fusion peptide encoded by both the 5′ polynucleotide and the 3′ polynucleotide. Collections of such in-frame fusion polynucleotides can vary in the percentage of fusion polynucleotides that contain upstream and downstream polynucleotides that are in-frame with respect to one another. The percentage in the total collection is at least 10% and can number 10%, 11%, 12%, 13%, 14%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% or any number in between.

Iterate/Iterative: In this application, to iterate means to apply a method or procedure repeatedly to a material or sample. Typically, the processed, altered or modified material or sample produced from each round of processing, alteration or modification is then used as the starting material for the next round of processing, alteration or modification. Iterative selection refers to a selection process that iterates or repeats the selection two or more times, using the survivors of one round of selection as starting material for the subsequent rounds.

Non-homologous: The term “non-homologous” in this application is defined as having sequence identity at the nucleotide level of less than 50%.

Open Reading Frame (ORF): An ORF is defined as any sequence of nucleotides in a nucleic acid that encodes a protein or peptide as a string of codons in a specific reading frame. Within this specific reading frame, an ORF can contain any codon specifying an amino acid, but does not contain a stop codon. The ORFs in the starting collection need not start or end with any particular amino acid. The ORF may be continuous or may be interrupted by introns.

Operably linked: The term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of effecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.

Percentage of sequence identity: The term “percent sequence identity” refers to the degree of identity between any given query sequence, e.g. SEQ ID NO: 102, and a subject sequence. A subject sequence typically has a length that is from about 80 percent to 200 percent of the length of the query sequence, e.g., 80, 82, 85, 87, 89, 90, 93, 95, 97, 99, 100, 105, 110, 115, or 120, 130, 140, 150, 160, 170, 180, 190 or 200 percent of the length of the query sequence. A percent identity for any subject nucleic acid or polypeptide relative to a query nucleic acid or polypeptide can be determined as follows. A query sequence (e.g. a nucleic acid or amino acid sequence) is aligned to one or more subject nucleic acid or amino acid sequences using the computer program ClustalW (version 1.83, default parameters), which allows alignments of nucleic acid or protein sequences to be carried out across their entire length (global alignment, Chenna 2003).

ClustalW calculates the best match between a query and one or more subject sequences, and aligns them so that identities, similarities and differences can be determined. Gaps of one or more residues can be inserted into a query sequence, a subject sequence, or both, to maximize sequence alignments. For fast pairwise alignment of nucleic acid sequences, the following default parameters are used: word size: 2; window size: 4; scoring method: percentage; number of top diagonals: 4; and gap penalty: 5. For multiple alignment of nucleic acid sequences, the following parameters are used: gap opening penalty: 10.0; gap extension penalty: 5.0; and weight transitions: yes. For fast pairwise alignment of protein sequences, the following parameters are used: word size: 1; window size: 5; scoring method: percentage; number of top diagonals: 5; gap penalty: 3. For multiple alignment of protein sequences, the following parameters are used: weight matrix: blosum; gap opening penalty: 10.0; gap extension penalty: 0.05; hydrophilic gaps: on; hydrophilic residues: Gly, Pro, Ser, Asn, Asp, Gln, Glu, Arg, and Lys; residue-specific gap penalties: on. The ClustalW output is a sequence alignment that reflects the relationship between sequences. ClustalW can be run, for example, at the Baylor College of Medicine Search Launcher website and at the European Bioinformatics Institute website on the World Wide Web (ebi.ac.uk/clustalw).

To determine a percent identity of a subject or nucleic acid or amino acid sequence to a query sequence, the sequences are aligned using Clustal W, the number of identical matches in the alignment is divided by the query length, and the result is multiplied by 100. It is noted that the percent identity value can be rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 are rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 are rounded up to 78.2.

Plasmid: The terms “plasmid” and “vector” refer to genetic elements used for carrying genes which are not a natural part of a cell or an organism. Vectors can either integrate into the genome or can be maintained extrachromosomally as linear or circular DNA fragments. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is useful for introducing polynucleotide sequences into a cell or an organism.

Phenotypic Value: Phenotypic value refers to a quantitative measure of a phenotype or a trait exhibited by an organism. For example, height measured in feet is a phenotypic value corresponding to body height in humans.

Promoter: The term “promoter” refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3′ to a promoter sequence. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental or physiological conditions. Promoters which cause a gene to be expressed in most cell types at most times are commonly referred to as “constitutive promoters”. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths may have identical promoter activity.

Random/Randomized: made or chosen without method or conscious decision.

Randomized In-frame Fusion Polynucleotides: As used herein, this phrase refers to polynucleotides in one or more starting populations fused to each other in a random manner to form randomized fusion polynucleotides, each randomized fusion polynucleotide comprising two or more members of the starting population(s). The random nature of the fusion is such that the association between different polynucleotides capable of fusing is not deliberately biased or directed, so that each starting polynucleotide has an equal or similar probability to be represented in the final population of fusion polynucleotides, and that it has an equal or similar probability to be fused with any other member of the starting population(s).

Randomized Translational Fusion: A randomized translational fusion is a process by which polynucleotides are randomly fused in a manner that the ORFs specified by the individual polynucleotide sequences are fused in-frame, to result in a fusion polynucleotide that encodes a fusion protein.

Randomly Fused: The term “randomly fused” refers to a process by which a collection of fused polynucleotides is generated from one or more collections of starting polynucleotides, where each member of the starting polynucleotide collection(s) has an equal or similar probability of joining to each other member. The objective of generating randomly fused polynucleotides is typically to generate all possible combinations, or as many combinations as possible, of fused members or sequences.

Resistance to a compound or stress, as described herein, implies that the cell is able to grow and divide under unfavorable conditions that would normally be inhibitive to growth.

Stringency of selection: The term “stringency of selection” refers to selection intensity, or the degree to which selective conditions affect the probability of an organism surviving the selection. A higher stringency of selection implies a higher selection intensity, with lower survival rates expected; a lower stringency of selection implies a lower selection intensity, with higher survival rates expected. Survival of a particular organism or population of organisms under selection ultimately depends on the fitness or viability of that organism or population of organisms under the selective conditions

Tolerance of a compound or stress, as described herein, implies that the cell is able to survive under unfavorable conditions that would normally be lethal to the cell.

Transformed: The term “transformed” means genetic modification by introduction of a polynucleotide sequence.

Transformation: As used herein the term “transformation” refers to the transfer of a nucleic acid fragment into a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic” or “recombinant” or “transformed” organisms.

Transformed Organism: A transformed organism is an organism that has been genetically altered by introduction of a polynucleotide sequence into the organism's genome.

The term unfavorable conditions as used herein implies any part of the growth condition, physical or chemical, that results in slower growth than under normal growth conditions, or that reduces the viability of cells compared to normal growth conditions.

The sequences of the 83 fusion polynucleotides are given in SEQ ID NO: 1-63 and 205-224; the amino acid sequence of the proteins encoded by the fusion polynucleotides are provided in SEQ ID NO: 64-126 and 225-244. These fusion polynucleotides are useful for developing alcohol and stress resistance and tolerance traits in a target organism. In general, expression of one or more of the fusion polynucleotides described herein can enhance stress and alcohol tolerance in a cell or organism.

Target organisms for the expression and use of the fusion polynucleotides described herein include but are not limited to: baker's yeast Saccharomyces cerevisiae; other Saccharomyces species; Schizosaccharomyces pombe; Kluyveromyces species such as K. lactis, K marxianus and K. thermotolerans; Candida species such as C. albicans, C. glabrata, C. stellate, C. tropicalis, C. dubliniensis and C. keroseneae; Pichia species such as P. angusta, P. anomala, P. membranifaciens and P. pastoris; oleaginous yeasts such as Yarrowia lipolytica; other yeast species such as Dekkera/Brettanomyces species; Brettanomyces bruxellensis; Torulaspora delbrueckii; Zygosaccharomyces bailii; and other yeasts, fungi, microbial eukaryotes and eukaryotic algae.

The 83 fusion polynucleotides described herein confer resistance or tolerance to a variety of stresses and unfavorable conditions, including, but not limited to high temperature; low temperature; low pH; high pH; high salt concentration; high osmotic strength; low osmotic strength; presence of oxidizing agents (hydrogen peroxide and other inorganic peroxides; inorganic oxidizing agents such as potassium permanganate; organic peroxides and hydroperoxides such as ethyl hydroperoxide, diacetyl peroxide, diethyl maleate, tert-butyl hydroperoxide, cumyl hydroperoxide and ascaridole); high pressure; low pressure; ionizing radiation such as ultraviolet, X-ray or gamma irradiation; presence of toxic metal ions such as those derived from the elements Ag (silver), As (arsenic), Cd (cadmium), Cr (chromium), Co (cobalt), Cu (copper), Hg (mercury), Ni (nickel), Pb (lead), Pt (platinum), Sb (antimony), Se (selenium), TI (thallium), or Zn (zinc); high concentrations of alcohols such as ethanol, propanol, iso-propanol, butanol, iso-butanol, alcohols with carbon chains exceeding 4 carbons; high concentrations of alkanes such as butane, pentane, hexane, heptane, octane, nonane, decane, undecane, dodecane, hexadecane, or isomers thereof; presence of furfural, 5-hydroxymethylfurfural, benzoic acid derivatives (for example p-hydroxybenzoic acid), and other toxic lignin breakdown products found in sugar preparations derived from biomass (Luo 2002); or unfavorable conditions or stresses caused by the presence of any other toxic compound or combinations of compounds, or any combination of the above.

In one embodiment, one or more of the fusion polynucleotides is combined with control elements such as a promoter and/or terminator in a manner that the promoter is upstream of the 5′ end of the fusion polynucleotide's coding region and the terminator is downstream of the 3′ end of the fusion polynucleotide' coding region. If the control elements are selected from such sequences that are known or suspected to be active in the target cell or organism, then the resulting expression constructs, or ‘expression cassettes’, each consisting of a promoter, a fusion polynucleotide, and a terminator, confer expression of the fusion polynucleotide when introduced into a cell.

Promoters used for expression of fusion polynucleotides may be strong promoters that result in high levels of protein expression, or weak promoters that result in low levels of protein expression, or promoters of intermediate strength. Promoters may also be constitutive, being expressed in all or most cells and in all or most stages of growth, or specific promoters whose activity depends on specific growth states or metabolic states. Inducible promoters, whose activity depends on the presence of a specific chemical or metabolite or growth condition which induces the promoter to be active, or repressible promoters, which can be shut off or reduced in activity in the presence of a specific chemical or metabolite or growth condition are also suitable. For example, a fusion polynucleotide encoding a fusion protein conferring stress tolerance can be expressed using a promoter that is induced under conditions of abiotic stress or in the presence of toxic and growth-inhibiting compounds in the growth medium.

Terminators used for expression of fusion polynucleotides may also vary in their activity. The function of a terminator in gene expression is in completing the transcription process and influencing mRNA half-life. Expression cassettes of fusion polynucleotides may contain strong or weak terminators or terminators of intermediate activity that predispose an mRNA to high, low or intermediate levels of stability. Such terminators are suitable for pairing with strong, weak or intermediate promoters.

The fusion polynucleotide expression cassettes may be further combined with sequences useful for propagation, or for selection of cell clones that have taken up DNA introduced into a population of cells. Such sequences may include, but are not limited to: centromeres, autonomously replicating elements, 2 micron plasmid origins of replication, prototrophic marker genes such as the S. cerevisiae genes URA3, TRP1, HIS3 or LEU2, or marker genes conferring resistance to antibiotics such as the kanamycin resistance gene conferring resistance to the aminoglycoside antibiotic G418 and related antibiotics.

Combinations of fusion polynucleotide expression cassettes and one or more sequences useful for propagation in the target organism may be inserted into a plasmid vector and cloned in E. coli or another suitable organism that allows propagation and replication of the joined polynucleotide sequences (Sambrook 1989). They may also be joined and then amplified using in vitro amplification methods such as the polymerase chain reaction.

Individual fusion polynucleotide expression cassettes combined with other sequences are then introduced into yeast in a manner that they become stably established as part of the yeast genome. There are a variety of suitable methods or introducing nucleic acids into yeast, including lithium acetate transformation (Gietz 2002, Gietz 2006, Gietz 2007), electroporation, spheroplast transformation, biolistic particle bombardment, and a glass bead method (Gietz 2001, Kawai 2010). Other methods of yeast transformation are also known, including use of 2 micron plasmids, and integrative transformation where the fusion polynucleotide is stably integrated within a yeast chromosome. In Saccharomyces cerevisiae, site-specific integration is routine and the integration site is dependent on sequences homologous to chromosomal sites that are present on the integrating nucleic acid.

After introduction into yeast, the population of yeast cells exposed to nucleic acid comprising the polynucleotide expression cassettes many be cultured in a medium allowing isolation of yeast clones that have taken up the polynucleotide expression cassettes and incorporated them into their genome. For example, if a fusion polynucleotide expression cassette is joined to a URA3 selectable marker gene and introduced into a ura-strain of yeast, then the resulting cell population, when plated on solid minimal media lacking uracil, will only allow growth of colonies that have stably taken up the URA3 selectable marker. If the URA3 selectable marker is covalently associated with yeast centromere sequences and a yeast autonomously replicating sequence as well as a fusion polynucleotide expression cassette, then the resulting yeast centromeric plasmid can become established in the yeast genome as a circular mini-chromosome, whose sequences are faithfully inherited during cell division.

In another embodiment, two or more fusion polynucleotides can be introduced into the same cell or organism to cause synergistic effects, and to result in a cell or an organism with higher levels of stress tolerance than observed when using only a single fusion polynucleotide. Such combinations of fusion polynucleotides can also arise in the process of screening a cell or an organism transformed with one or more fusion polynucleotides for enhanced resistance to or tolerance of stresses and toxic compounds by transforming this organism with a library of fusion polynucleotides and screening the resulting transformants for higher levels of resistance or tolerance.

After delivery of a fusion polynucleotide and its control sequences into a cell, and its selection for presence in the cell, a variety of tests for resistance to and tolerance of stresses and toxic compounds are performed, which typically include exposure of a cell population to an unfavorable condition for a specified period of time and monitoring of the cell population during or after exposure. Changes in growth rate or cell viability are measured by comparing transformed cells to untransformed control cells or cells transformed with a control nucleic acid, such as an empty expression vector or a gene known not to confer resistance or tolerance phenotypes.

The fusion polynucleotides described herein can be used with yeast strains used for fermentation or the production of fuels or chemicals. Fermentation and fuel or chemical production often involve culturing the cells in the presence of compounds that inhibit growth, compounds that reduce cell viability, or abiotic conditions including but not limited to high temperature, high salt, low pH or high pH that also either inhibit growth or reduce cell viability or cell productivity or combinations thereof.

The fusion polynucleotides are also useful for modifying industrial yeast strains used for the production of ethanol, other alcohols, or a variety of chemicals.

Among the fusion polynucleotides listed herein are 61 different fusion polynucleotides containing the yeast full length WHI2 open reading frame. The WHI2 gene (Saul 1985, Mountain 1990, Mountain 1990a, Radcliffe 1997, Kaida 2002, Leadsham 2009, Mendl 2011, Müller 2011), has been previously implicated in stress tolerance (Mendl 2011, Müller 2011) as well as a variety of other cellular processes including regulation of colony morphology, control of cell division and cell size, nutritional sensing, and mitochondrial function.

Among the fusion polynucleotides listed herein are two fusion polynucleotides (M21-A09, M24-B12; SEQ ID NO:31 and 44) and their corresponding fusion proteins (SEQ ID NO:94 and 107) which represent fusions of the WHI2 protein with phosphatases.

Among the fusion polynucleotides listed herein are 14 fusion polynucleotides (Y1-38A, SEQ ID NO:15; M22-C05, SEQ ID NO: 35; M23-C03, SEQ ID NO:37; M27-B07, SEQ ID NO: 56; PP0219-223, SEQ ID NOS: 205-209; and PP0229-233, SEQ ID NOS: 215-219) and their corresponding fusion proteins (Y1-38A, SEQ ID NO:78; M22-C05, SEQ ID NO: 98; M23-C03, SEQ ID NO:100; M27-B07, SEQ ID NO: 119; PP0219-223, SEQ ID NOS: 225-229; and PP0229-233, SEQ ID NOS: 235-239) which represent fusions of the WHI2 protein with members of the KEOPS complex, a conserved protein complex with a role in telomere maintenance, but of largely unknown function (Bianchi 2006, Downey 2006).

Among the fusion polynucleotides listed herein are 11 fusion polynucleotides (M21-008, SEQ ID NO: 32; PP0224-228, SEQ ID NOS: 210-214; and PP0234-238, SEQ ID NOS: 220-224) and their corresponding fusion proteins (M21-008, SEQ ID NO: 95; PP0224-228, SEQ ID NOS: 230-234; and PP0234-238, SEQ ID NOS: 240-244) which represent fusions of the WHI2 protein with members of the EGO complex, a vacuolar membrane-associated protein complex with a role in activation of microautophagy during exit from rapamycin-induced growth arrest (Dubouloz 2005, Gao 2006, Piper 2006).

The sequences of 83 fusion polynucleotides are given in SEQ ID NO: 1-63 and 205-224; the sequences of the fusion proteins that they encode are given in SEQ ID NO: 64-126 and 225-244.

Table 1 shows a summary of all 83 fusion polynucleotides and their component ORFs

TABLE 1 Yeast active fusion polynucleotides + component open reading frames (ORFs) Fusion Nucleic poly- acid Protein 5′ 5′ 5′ 3′ 3′ 3′ nucleotide SEQ SEQ ORF ORF ORF ORF ORF ORF name ID ID ID name description ID name description Y1-5A 1 64 YDR246W-A Putative protein YOR043W WHI2 Activator of the of unknown general stress function response Y1-7A 2 65 YHR126C ANS1 Putative protein YOR043W WHI2 Activator of the of unknown general stress function response Y1-9A 3 66 YOL026C MIM1 Mitochondrial YDL159W STE7 Signal transducing outer membrane MAP kinase protein kinase Y1-13A 4 67 YDR488C PAC11 Dynein YOR043W WHI2 Activator of the intermediate general stress chain response Y1-17A 5 68 YOR043W WHI2 Activator of the YJL185C YJL185C Putative protein of general stress unknown function response Y1-18A 6 69 YLR375W STP3 Zinc-finger YOR085W OST3 Oligosaccharyl- protein transferase of unknown gamma subunit function Y1-19A 7 70 YOR043W WHI2 Activator of the YFL066C YFL066C Y' element general stress helicase-like response protein Y1-20A 8 71 YHL028W WSC4 ER membrane YOR043W WHI2 Activator of the protein general stress involved in response translocation Y1-21A 9 72 YOL054W PSH1 E3 ubiquitin YLR094C GIS3 Protein of ligase unknown function Y1-23A 10 73 YFL066C YFL066C Y' element YOR043W WHI2 Activator of the helicase-like general stress protein response Y1-25A 11 74 YGR060W ERG25 C-4 methyl YOR043W WHI2 Activator of the sterol general stress oxidase response Y1-28A 12 75 YJL065C DLS1 ISW2 chromatin YOR043W WHI2 Activator of the accessibility general stress complex subunit response Y1-33A 13 76 YLR094C GIS3 Protein of YKL117W SBA1 Hsp90 unknown family co- function chaperone Y1-34B 14 77 YML064C TEM1 GTP-binding YOR043W WHI2 Activator of the protein of general stress the ras response superfamily Y1-38A 15 78 YML036W CGI121 Component of YOR043W WHI2 Activator of the the KEOPS general stress protein response complex Y1-39B 16 79 YLR466C-B YLR466C-B Dubious open YOR043W WHI2 Activator of the reading frame general stress response Y1-40A 17 80 YDL109C YDL109C Putative lipase; YOR043W WHI2 Activator of the involved in lipid general stress metabolism response Y1-43A 18 81 YLR154C-G YLR154C-G Putative protein YOR043W WHI2 Activator of the of unknown general stress protein response Y1-45A 19 82 YIR016W YIR016W Putative protein YOR043W WHI2 Activator of the of unknown general stress protein response Y1-47A 20 83 YER018C SPC25 Kinetochore-assoc. YOR043W WHI2 Activator of the Ndc80 complex general stress component response Y1-48A 21 84 YML116W ATR1 Multidrug YOR043W WHI2 Activator of the efflux general stress pump response Y1-49A 22 85 YLR094C GIS3 Protein of YHR219W YHR219W Putative unknown helicase function Y1-58B 23 86 YDR378C LSM6 Lsm (Like Sm) YBL075C SSA3 ATPase protein involved in protein folding, stress response Y1-58C 24 87 YDR462W MRPL28 Mitochondrial YGL236C MTO1 Mitochondrial large subunit protein ribosomal protein Y1-66C 25 88 YGL235W YGL235W Putative YLR369W SSQ1 Mitochondrial protein of hsp70- unknown type molecular function chaperone Y1-67B 26 89 YLL039C UBI4 Ubiquitin YBL081W YBL081W Non-essential essential protein of for the cellular unknown stress response function Y2-28A 27 90 YLR154C-G YLR154C-G Putative YOL060C MAM3 Protein protein of required for unknown mitochondrial function morphology M21-A02 28 91 YOR043W WHI2 Activator YHR203C RPS4B 40S ribosomal of the general subunit stress protein response M21-A03 29 92 YOR043W WHI2 Activator of the YLR094C GIS3 Protein of general stress unknown response function M21-A04 30 93 YGR209C TRX2 Cytoplasmic YOR043W WHI2 Activator of the thioredoxin general stress isoenzyme response M21-A09 31 94 YGR203W YCH1 Phosphatase YOR043W WHI2 Activator of the similar to general stress Cdc25p response M21-C08 32 95 YBR077C SLM4 Component of the YOR043W WHI2 Activator of the EGO protein general stress complex response M21-D06 33 96 YNL086W SNN1 Putative protein of YOR043W WHI2 Activator of the unknown function general stress response M22-C01 34 97 YPR080W TEF1 Translational YOR043W WHI2 Activator of the elongation factor general stress EF-1 alpha response M22-005 35 98 YKR095W-A PCC1 Component of the YOR043W WHI2 Activator of the KEOPS protein general stress complex response M22-D01 36 99 YIR015W RPR2 Subunit of nuclear YOR043W WHI2 Activator of the RNase P general stress response M23-CO3 37 100 YJL184W GON7 Component of the YOR043W WHI2 Activator of the KEOPS protein general stress complex response M23-D02 38 101 YPL250C ICY2 Protein of YJL205C NCE101 Protein of unknown unknown function function M23-D09 39 102 YMR226C YMR226C NADP(+)- YBR195C MSI1 Subunit of dependent chromatin dehydrogenase assembly factor I M23-E02 40 103 YEL034W HYP2 Translation YOR043W WHI2 Activator of the elongation factor general stress eIF-5A response M23-F02 41 104 YPL250C ICY2 Protein of YOR043W WHI2 Activator of the unknown general stress function response M23-H01 42 105 YLR154C-G YLR154C-G Putative YGR063C SPT4 Pol I and Pol II protein of transcriptional unknown regulator function M24-A05 43 106 YNR049C MSO1 Secretory vesicle YOR043W WHI2 Activator of the docking complex general stress component response M24-B12 44 107 YMR156C TPP1 DNA 3'- YOR043W WHI2 Activator of the phosphatase general stress response M24-D11 45 108 YBR195C MSI1 Subunit of YOR101W RAS1 G-protein chromatin signaling assembly factor I GTPase M24-E05 46 109 YGR203W YCH1 Phosphatase YLR094C GIS3 Protein of similar to unknown Cdc25p function M24-F06 47 110 YHR055C CUP1-2 Metallothionein YOR043W WHI2 Activator of the binding copper general stress and cadmium response M25-E1 48 111 YJR120W YJR120W Protein of YOR043W WHI2 Activator of the unknown general stress function response M25-F4 49 112 YHR055C CUP1-2 Metallothionein YOR043W WHI2 Activator of the general stress response M25-G8 50 113 YPR062W FCY1 Cytosine YOR043W WHI2 Activator of the deaminase general stress response M25-G10 51 114 YMR195W ICY1 Protein of YBR195C MSI1 Subunit of unknown chromatin function assembly factor I M25-H11 52 115 YMR195W YLR162W Putative YOR043W WHI2 Activator of the protein of general stress unknown response function M26-Al2 53 116 YMR195W ICY1 Protein of YOR043W WHI2 Activator of the unknown general stress function response M26-D6 54 117 YNL259C ATX1 Cytosolic copper YOR043W WHI2 Activator of the metallochaperone general stress response M27-A1 55 118 YDR432W NPL3 RNA-binding YOR043W WHI2 Activator of the protein general stress response M27-B7 56 119 YOR043W WHI2 Activator of the YML036W CGI121 Component general stress of the KEOPS response protein complex M27-F8 57 120 YDR24 YDR246W-A Putative YHR008C S0D2 Mitochondrial protein of manganese unknown superoxide function dismutase M28-A4 58 121 YER018C SPC25 Kinetochore- YNL042W-B YNL042W-B Putative assoc. Ndc80 protein of complex unknown component function M28-C9 59 122 YDR246W-A YDR246W-A Putative YPL157W TGS1 Trimethyl protein of guanosine unknown synthase function M28-D6 60 123 YBR197C YBR197C Putative YLR094C GIS3 Protein of protein of unknown unknown function function M28-E4 61 124 YDR378C LSM6 Lsm (Like Sm) YLR094C GIS3 Protein of protein unknown function M29-E7 62 125 YGR063C SPT4 Pol I and Pol II YOR043W WHI2 Activator of the transcriptional general stress regulator response M30-E11 63 126 YLR044C PDC1 Pyruvate YIL033C BCY1 cAMP-dep decarboxylase protein kinase regulatory subunit PP0219 205 225 YGR262C BUD32 Component YOR043W WHI2 Activator of the of the KEOPS general stress protein response complex PP0220 206 226 YJL184 GON7 Component YOR043W WHI2 Activator of the of the KEOPS general stress protein response complex PP0221 207 227 YKR038C KAE1 Component YOR043W WHI2 Activator of the of the KEOPS general stress protein response complex PP0222 208 228 YKR095W-A PCC1 Component YOR043W WHI2 Activator of the of the KEOPS general stress protein response complex PP0223 209 229 YML036W CGI121 Component YOR043W WHI2 Activator of the of the KEOPS general stress protein response complex PP0224 210 230 YBR077C SLM4 Component YOR043W WHI2 Activator of the of the KEOPS general stress protein response complex PP0225 211 231 YGR163W GTR2 Component YOR043W WHI2 Activator of the of the KEOPS general stress protein response complex PP0226 212 232 YKL143W LTV1 Component YOR043W WHI2 Activator of the of the EGO general stress protein response complex PP0227 213 233 YKR007W MEH1 Component YOR043W WHI2 Activator of the of the EGO general stress protein response complex PP0228 214 234 YML121W GTR1 Component YOR043W WHI2 Activator of the of the EGO general stress protein response complex PP0229 215 235 YOR043W WHI2 Activator of the YGR262C BUD32 Component general stress of the KEOPS response protein complex PP0230 216 236 YOR043W WHI2 Activator of the YJL184W GON7 Component general stress of the KEOPS response protein complex PP0231 217 237 YOR043W WHI2 Activator of the YKR038C KAE1 Component general stress of the KEOPS response protein complex PP0232 218 238 YOR043W WHI2 Activator of the YKR095W-A PCC1 Component general stress of the KEOPS response protein complex PP0233 219 239 YOR043W WHI2 Activator of the YML036W CGI121 Component general stress of the KEOPS response protein complex PP0234 220 240 YOR043W WHI2 Activator of the YBR077C SLM4 Component general stress of the EGO response protein complex PP0235 221 241 YOR043W WHI2 Activator of the YGR163W GTR2 Component general stress of the EGO response protein complex PP0236 222 242 YOR043W WHI2 Activator of the YKL143W LTV1 Component general stress of the EGO response protein complex PP0237 223 243 YOR043W WHI2 Activator of the YKR007W MEH1 Component general stress of the EGO response protein complex PP0238 224 244 YOR043W WHI2 Activator of the YML121W GTR1 Component general stress of the response EG + A2:I85

EXAMPLES Example 1: Generation of Fusion Polynucleotides Encoding Fusion Polypeptides

A yeast fusion polynucleotide library was generated according to the method set forth in U.S. application Ser. No. 14/134,619, which is hereby incorporated by reference in its entirety.

Example 2: Resistance and Tolerance Phenotypes in Galactose-Containing Media of Yeast Strains Transformed with Fusion Polynucleotide Centromeric Plasmids

All fusion polynucleotides generated from Example 1 were cloned into a derivative of the yeast centromeric plasmid p416-GAL1 (Mumberg 1995, Funk 2002). The yeast centromeric plasmid p416-GAL1 contains the following sequences for plasmid propagation in yeast and/or E. coli and expression of an inserted polynucleotide: the bacterial replicon of plasmid pMB1, the bacterial ampicillin-resistance gene, the yeast CEN6/ARSH4 cassette (Sikorski 1989) containing the chromosome 6 centromere and the yeast histone H4-associated autonomously replicating sequence (ARS), the yeast URA3 prototrophic marker gene, and the yeast GAL1 promoter and CYC1 terminator placed adjacent to each other in a manner that allows expression of coding regions inserted therebetween. The nucleotide sequence of the p416-GAL1 derivative is SEQ ID NO 127. All polynucleotides were cloned between nucleotide numbers 3206 and 3207 of SEQ ID NO 127.

The resulting set of centromeric plasmids containing expression cassettes of the 63 fusion polynucleotides under control of the S. cerevisiae GAL1 promoter (SEQ ID NO: 1-63) are hereafter referred to as ‘fusion polynucleotide GAL1 centromeric plasmids’. Individual fusion polynucleotide GAL1 centromeric plasmids are referred to by the SEQ ID number of the fusion polynucleotide contained therein, i.e. ‘fusion polynucleotide GAL1 centromeric plasmid #5’ corresponds to SEQ ID NO: 5 cloned between nucleotide numbers 3206 and 3207 of the p416-GAL1 vector (SEQ ID NO 127).

All experiments measuring tolerance and resistance activities of the fusion polynucleotides were performed using strain BY4741 (Brachmann 1998) transformed with each fusion polynucleotide GAL1 centromeric plasmid.

Yeast transformations were performed by the lithium acetate-heat shock method (Gietz 2002, Gietz 2006, Gietz 2007). The yeast strain BY4741 (Brachmann 1998) from a plate or an overnight culture was inoculated into 50 ml of YPD medium (for 1 L medium, 20 g Bacto Peptone, 10 g Bacto Yeast Extract are combined and after autoclaving 20 g Glucose are added as a 20% sterile solution) at 30° C. on a shaker at 225 rpm from a starting density of 5×10⁶ cells/ml (cell density determined with a hemocytometer), and grown over several hours to a final cell density of 2×10⁷ cells/ml. The cells were harvested by centrifuging at 3000 g for 5 min, were then resuspended in 25 ml of sterile deionized water, and centrifuged again. Cells were resuspended in 1 ml of sterile water, transferred to a 1.5 ml microcentrifuge tube, centrifuged for 30 sec at 3000 rpm and the supernatant aspirated. The cell pellet was then resuspended in 0.4 ml of sterile deionized water. The cell suspension was combined with 3.26 ml of transformation mix (2.4 ml of 50% w/v PEG 3350, 360 μl 1M Lithium acetate and 500 μl 10 mg/ml sheared, boiled salmon sperm DNA) and mixed well. Aliquots of DNA (100 ng-1 μg) were pipetted into separate 1.5 ml microcentrifuge tubes and combined with 380 μl of the cell suspension in transformation mix. The cell/DNA mixture was mixed thoroughly and incubated at 42° C. on a shaker at 250 rpm for 40 minutes. The transformations were then centrifuged for 1 minute at 3000 rpm in a microcentrifuge, the supernatant aspirated and each cell aliquot resuspended in 0.5-1 ml sterile deionized water. Depending on the desired density of colonies, 10 μl to 1 ml of the cell suspension were plated with sterile 4 mm glass beads onto one 10 cm or 15 cm plate containing synthetic complete uracil dropout solid medium having glucose as a carbon source (SCD-Ura agar; for 1 L, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix and 15 g Bacto agar are combined, the pH is adjusted with 120 μl 10N NaOH to bring the pH to 5.6-5.8, and after autoclaving 20 g glucose are added as a 20% sterile solution). After drying, the plates were covered and incubated at 30° C. for 3-4 days until colonies of transformants had formed. The individual fusion polynucleotide GAL1 centromeric plasmid transformants of strain BY4741 were maintained on SCD-Ura agar.

Resistance to and tolerance of the 64 yeast strains containing fusion polynucleotides (63 fusion polynucleotide GAL1 centromeric plasmids and one control vector) to heat (42° C.), ethanol (15%), butanol (3%), salt (2M NaCl) and low pH (pH 3.0 in 0.2M sodium acetate) were measured in triplicate.

The 64 strains were first cultured for 16 hours at 30° C., 800 rpm with a 3 mm radius of gyration in 96-well plates (2 ml square wells) in synthetic complete uracil dropout medium containing glucose and galactose as carbon sources (SCDGal-Ura; for 1 L of medium, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix, and 5 g glucose are combined, the pH is adjusted to 5.6-5.8 by the addition of 120 μl 10N NaOH and after autoclaving 5 g glucose and 15 g galactose are added as sterile 20% solutions). The cell density was then measured with a hemocytometer, and the cells diluted in fresh 96-well plates (2 ml square wells) to a final cell density of 1×10⁷ cells/ml in 1.25 ml YPGal (for 1 L of medium, 20 g Bacto Peptone and 10 g Bacto Yeast Extract are combined, and after autoclaving 20 g galactose are added as a sterile 20% solution). The cells were cultured for an additional 5 hours.

The cell suspensions were then added in 0.25 ml aliquots to new 96-well plates (2 ml square wells), each well containing 0.25 ml of YPGal medium with a 2× concentration of one selective agent. The selective agents used were: NaCl at a final concentration of 2M; ethanol at a final concentration of 15%; n-butanol at a final concentration of 3%; or sodium acetate pH 3.0 at a final concentration of 0.2M. The sodium acetate was prepared as a 1M solution of sodium acetate pH 3.0 by mixing 2.74 ml glacial acetic acid with 0.11 g anhydrous sodium acetate in 50 ml final volume and filter sterilized using a 0.2 micron filter. For measuring heat tolerance, the 0.25 ml aliquots of cell suspension were combined with 0.25 ml of YPGal and cultured in 96-well plates (2 ml square wells) at 42° C. All selective cultures were incubated for 3 days: those measuring heat tolerance at 42° C. and all others at 30° C. The cultures were then spotted undiluted and in 1:10 dilutions onto fresh 15 cm plates containing YPD solid medium (for 1 L medium, 20 g Bacto Peptone, 10 g Bacto Yeast Extract and 15 g Bacto Agar are combined, and after autoclaving 20 g glucose are added as a sterile 20% solution). Spotting was conducted using a Bel-Art 96-well replicating tool (Bel-Art Products) that deposits spots of approximately 3 μl from each well onto the recipient plate. Dilutions were made in synthetic complete uracil dropout medium containing glucose as a carbon source (SCD-Ura; for 1 L of medium, 6.7 g yeast nitrogen base and 0.77 g uracil dropout mix are combined, the pH is adjusted to 5.6-5.8 by the addition of 120 μl 1 ON NaOH and after autoclaving 20 g glucose are added as a sterile 20% solution).

The spots were allowed to dry, the plates incubated at 30° C. for 1 day to allow surviving cells to grow into cell spots or individual colonies. The cell density of surviving cells from each transformant for each selective condition was scored on a relative scale from 0-3, 0 being no growth, 1 being slight growth, 2 being significant growth and 3 being confluent growth. Both the undiluted and diluted spots were taken into account to generate the score. Triplicate measurements were made for each condition and control.

To obtain a final activity score for each fusion polynucleotide GAL1 centromeric plasmid and each selective condition, the triplicate scores for each selective condition were added, and the triplicate score for the control plasmid subtracted. Final activity scores below zero were scored as zero. All scores are shown in Table 2 under the columns labeled ‘Activity scores (rich medium)’.

Resistance and tolerance of the 64 yeast strains to ethanol and butanol were also measured in minimal media containing raffinose and galactose as carbon sources. Here, the 64 strains were first grown in 96 well plates (2 ml square wells) containing minimal uracil dropout medium containing 2% raffinose as a carbon source (SCRaf-Ura; for 1 L of medium, 6.7 g yeast nitrogen base and 0.77 g uracil dropout mix are combined; pH is adjusted to 5.6-5.8 by the addition of 120 μl 10N NaOH and after autoclaving 20 g raffinose are added as a sterile 20% solution). Cells were incubated for 6 hours at 30° C. with constant shaking at 200 rpm. Expression of the fusion genes was then induced with galactose at a final concentration of 2% and incubation continued overnight. Subsequently, 0.1 OD cultures from each well were inoculated into minimal uracil dropout medium containing 1% raffinose and 2% galactose containing different concentrations of ethanol and butanol. Four concentrations each of ethanol (i.e. 8%, 11%, 14% and 17% v/v) and n-butanol (2%, 2.5%, 3% and 3.5% v/v) were used.

The 96-well culture plates (2 ml square wells) were covered with air-permeable sealing films and all plates were together further sealed in a large airtight plastic bag. This created a semi-aerobic condition and the cultures were incubated in a shaking incubator at 30° C. for 3 days. Using a Bel-Art 96-well replicating tool (Bel-Art Products) two dilutions of each culture (1:10 and 1:100) were spotted on minimal uracil dropout solid medium containing glucose as a carbon source (SCD-Ura agar; for 1 L of medium, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix, and 15 g Bacto Agar are combined, the pH is adjusted to 5.6-5.8 by the addition of 120 μl 10N NaOH and after autoclaving 20 g glucose are added as a sterile 20% solution). The plates were incubated at 30° C. for 2 days.

An image was taken of each plate and was scored for each dilution for each fusion polynucleotide. A score of 0 to 5 was given to each spot based on growth compared to the negative control strain. For each fusion polynucleotide GAL1 centromeric plasmid and for each dilution, the score was multiplied by its corresponding concentration of butanol/ethanol and averaged. The same scoring method was followed for the strain with the negative control plasmid on the same plates: this provided the background. The final score was obtained by subtracting the average score of the negative control strain from the average score of the strain with the individual fusion polynucleotide GAL1 centromeric plasmids. All scores are shown in Table 2 under the columns labeled ‘Activity scores (minimal medium)’.

Yeast strain BY4741, when transformed with each of the 63 fusion polynucleotide GAL1 centromeric plasmids, showed significant resistance to or tolerance of elevated temperature, ethanol, butanol, low pH and/or high salt compared to the negative control plasmid p416-GAL1, as shown in Table 2 below.

All resistance and tolerance scores above background are listed in Table 2 below.

TABLE 2 Resistance and tolerance activities of 63 fusion polynucleotides in galactose-containing rich medium in S. cerevisiae Fusion gene Fusion Activity nucleic gene Activity scores (rich medium) scores Fusion acid protein pH 3 (minimal poly- sequence sequence (0.1M Salt medium) nucleotide SEQ SEQ Heat Ethanol Butanol sodium (2M Butanol Ethanol name ID ID (42° C.) (15%) (3%) acetate) NaCl) (3%) (15%) Y1-5A 1 64 3.75 0.00 4.75 2.75 4.75 0.0 35.0 Y1-7A 2 65 3.75 1.75 7.75 7.75 7.75 0.0 3.5 Y1-9A 3 66 0.00 1.75 4.75 4.75 4.75 0.0 0.8 Y1-13A 4 67 5.75 2.75 10.75 6.75 6.75 0.0 10.5 Y1-17A 5 68 6.75 2.75 7.75 8.75 7.75 0.0 7.0 Y1-18A 6 69 0.00 0.00 1.75 2.75 3.75 0.0 0.0 Y1-19A 7 70 0.75 5.75 7.75 8.75 7.75 0.0 9.8 Y1-20A 8 71 6.75 0.00 3.75 2.75 2.75 0.0 23.8 Y1-21A 9 72 5.75 0.00 4.75 5.75 7.75 0.0 0.0 Y1-23A 10 73 6.75 0.00 4.75 5.75 4.75 0.0 0.8 Y1-25A 11 74 0.75 0.00 1.75 2.75 1.75 0.0 7.0 Y1-28A 12 75 3.75 2.75 5.75 7.75 6.75 0.0 17.5 Y1-33A 13 76 6.75 0.00 0.00 1.75 4.75 0.0 0.0 Y1-34B 14 77 6.75 5.75 7.75 8.75 7.75 0.0 14.0 Y1-38A 15 78 6.75 2.75 7.75 8.75 4.75 0.0 7.0 Y1-39B 16 79 6.75 3.75 7.75 6.75 5.75 0.0 14.0 Y1-40A 17 80 5.75 0.00 1.75 5.75 4.75 0.0 7.0 Y1-43A 18 81 6.75 5.75 6.75 8.75 7.75 0.0 14.0 Y1-45A 19 82 6.75 0.00 0.00 0.00 1.75 0.0 0.0 Y1-47A 20 83 8.75 5.75 4.75 4.75 4.75 0.0 14.8 Y1-48A 21 84 6.75 5.75 4.75 8.75 7.75 0.0 10.5 Y1-49A 22 85 1.75 0.00 0.00 0.00 1.75 0.0 0.0 Y1-58B 23 86 0.00 0.00 0.00 0.00 0.00 0.0 0.0 Y1-58C 24 87 0.00 0.00 0.00 0.00 0.00 0.0 0.0 Y1-66C 25 88 0.00 0.00 0.00 0.00 0.00 0.0 0.0 Y1-67B 26 89 0.75 0.00 0.00 0.00 2.75 3.0 0.0 Y2-28A 27 90 0.75 0.00 0.00 0.00 0.00 0.0 0.0 M21-A02 28 91 3.75 2.75 4.75 7.25 7.75 4.5 0.0 M21-A03 29 92 6.75 5.75 10.75 11.75 7.75 16.0 0.0 M21-A04 30 93 6.75 0.00 4.75 5.75 4.75 4.5 0.0 M21-A09 31 94 5.75 2.75 4.75 4.75 3.75 4.5 2.8 M21-C08 32 95 6.75 2.75 6.25 5.75 4.75 4.5 2.8 M21-D06 33 96 7.75 0.00 4.00 3.25 9.75 1.0 0.0 M22-C01 34 97 6.75 3.00 7.00 9.25 9.75 16.4 0.0 M22-C05 35 98 6.75 3.00 8.00 6.25 6.75 2.5 0.0 M22-D01 36 99 4.75 3.00 7.00 6.25 9.75 3.0 0.0 M23-C03 37 100 9.75 9.00 10.00 9.25 9.75 11.8 0.0 M23-D02 38 101 0.00 0.00 0.00 3.25 6.75 0.0 0.0 M23-D09 39 102 0.00 9.00 10.00 12.25 12.75 6.5 0.0 M23-E02 40 103 9.75 1.00 5.00 6.25 6.75 3.5 0.0 M23-F02 41 104 9.75 9.00 10.00 12.25 12.75 1.6 0.8 M23-H01 42 105 2.75 0.00 3.00 6.25 6.75 0.0 0.0 M24-A05 43 106 0.75 3.00 7.00 6.25 9.75 3.5 13.0 M24-B12 44 107 3.75 0.00 3.00 6.25 9.75 4.5 4.3 M24-D11 45 108 0.00 3.00 10.00 6.25 3.75 18.3 0.0 M24-E05 46 109 0.00 6.00 7.00 12.25 12.75 14.9 0.0 M24-F06 47 110 6.75 6.00 7.00 9.25 9.75 7.8 0.0 M25-E1 48 111 9.75 3.00 4.00 6.25 9.75 4.0 0.0 M25-F4 49 112 9.75 0.00 0.00 6.25 6.75 2.5 0.0 M25-G8 50 113 9.75 0.00 1.00 6.25 6.75 2.5 0.0 M25-G10 51 114 1.75 6.00 1.00 8.25 8.75 0.0 0.0 M25-H11 52 115 6.75 0.00 0.00 1.25 4.75 2.5 0.0 M26-A12 53 116 9.75 9.00 10.00 12.25 12.75 19.1 14.3 M26-D6 54 117 9.75 0.00 0.00 6.25 5.75 20.0 17.8 M27-A1 55 118 6.75 9.00 4.00 12.25 12.75 20.0 21.3 M27-B7 56 119 9.75 0.00 1.00 6.25 6.75 5.6 0.0 M27-F8 57 120 0.00 0.00 0.00 0.00 0.75 0.8 0.0 M28-A4 58 121 0.00 0.00 0.00 0.00 3.75 0.0 0.0 M28-C9 59 122 0.00 0.00 0.00 0.00 6.75 0.0 0.0 M28-D6 60 123 3.75 0.00 4.00 6.25 9.75 2.5 0.0 M28-E4 61 124 3.75 3.00 4.00 9.25 12.75 0.0 0.0 M29-E7 62 125 6.75 3.00 7.00 9.25 7.75 4.4 7.0 M30-E11 63 126 0.75 0.00 0.00 0.25 8.25 13.0 0.0 p416-GAL1 0.00 0.00 0.00 0.00 0.00 0.0 0.0

Example 3: Resistance and Tolerance Phenotypes in Glucose-Containing Media of Yeast Strains Transformed with Fusion Polynucleotide Centromeric Plasmids

63 fusion polynucleotides (SEQ ID NO: 1-63) were cloned into the yeast expression vector p466-TEF1 (SEQ ID NO: 128), which is similar to the yeast centromeric plasmid p416-TEF1 (Mumberg 1995, Funk 2002). The yeast centromeric plasmid p466-TEF1 contains the following sequences for plasmid propagation in yeast and E. coli, and expression of an inserted polynucleotide: the bacterial replicon of plasmid pMB1; the bacterial ampicillin-resistance gene; the yeast CEN6/ARSH4 cassette (Sikorski 1989) containing the chromosome 6 centromere and the yeast histone H4-associated autonomously replicating sequence (ARS); the yeast URA3 prototrophic marker gene; and the yeast TEF1 promoter placed adjacent to the CYC1 terminator in a manner that allows expression of coding regions placed between them. All polynucleotides were cloned between nucleotides 3029 and 3030 of SEQ ID NO 128.

The resulting set of constructs are referred to as ‘fusion polynucleotide TEF1 centromeric plasmids’. Each contains an expression cassette of one of 63 fusion polynucleotides (SEQ ID NO: 1-63) under control of the S. cerevisiae TEF1 promoter. All experiments measuring tolerance and resistance activities of the fusion polynucleotides were performed by using strain BY4741 (Brachmann 1998) that was transformed with each fusion polynucleotide centromeric plasmid. Yeast transformations were performed using the lithium acetate-heat shock method as described in Example 2. The individual fusion polynucleotide centromeric plasmid transformants of strain BY4741 were maintained on minimal uracil dropout solid medium containing glucose as a carbon source (SCD-Ura agar; for 1 L medium, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix, and 15 g Bacto Agar are combined, the pH is adjusted to 5.6-5.8 with 120 μl 10N NaOH and after autoclaving 20 g of glucose are added as a sterile 20% solution). Quantitative determinations of ethanol and butanol tolerance was conducted in rich medium containing glucose as a carbon source. Individual fusion polynucleotide centromeric plasmids are referred to by the SEQ ID number of the fusion polynucleotide contained therein, i.e. ‘fusion polynucleotide TEF1 centromeric plasmid #5’ corresponds to SEQ ID NO 5 cloned between nucleotide numbers 3029 and 3030 of the p466-TEF1 vector.

Resistance and tolerance of the 64 yeast strains (63 harboring the fusion polynucleotide constructs plus one strain with the control vector) were tested for resistance and tolerance to heat (42° C.), ethanol (15%), butanol (3%) and low pH (pH 3.0 in 0.2M sodium acetate). Measurements were taken in quadruplicate; that is, two independent transformants of each fusion polynucleotide centromeric plasmids were each tested in duplicate. Here, the 63 fusion polynucleotide strains and one control strain were first cultured in 96-well plates (2 ml square wells) having 1 ml per well of synthetic complete uracil dropout medium containing glucose as a carbon source (SCD-Ura: for 1 L of medium, 6.7 g yeast nitrogen base and 0.77 g uracil dropout mix are combined, the pH is adjusted to 5.6-5.8 by the addition of 120 μl 10N NaOH, and after autoclaving 20 g glucose are added as a sterile 20% solution). Cells were incubated for 16 hours at 30° C. with shaking at 800 rpm with a 3 mm radius of gyration.

The cell densities were measured with a hemocytometer, the cell suspensions diluted in a fresh 96-well plate (2 ml square wells) to a final cell density of 1×10⁷ cells/ml in 1.25 ml SCD-Ura, and then grown for an additional 2 hours under the same conditions. The cell suspensions were then added in 0.25 ml aliquots to fresh 96-well plates (2 ml square wells) and each aliquot combined with 0.25 ml YPD medium (for 1 L of medium, 20 g Bacto Peptone and 10 g Bacto Yeast Extract are combined, and after autoclaving 20 g glucose are added as a sterile 20% solution) containing a 2× concentration of one selective agent. The selective agents used were: ethanol at a final concentration of 15%; n-butanol at a final concentration of 3%, or sodium acetate pH 3.0 at a final concentration of 0.2M. The sodium acetate was prepared as a 1M solution by mixing 2.74 ml glacial acetic acid with 0.11 g anhydrous sodium acetate in 50 ml final volume and filter sterilized using a 0.2 micron filter. For measuring heat tolerance, the 0.25 ml aliquots of cell suspension were combined with 0.25 ml of SCD-Ura medium and cultured in 96-well plates (2 ml square wells) at 42° C. All selective cultures were incubated for 48 hours; those measuring heat tolerance at 42° C. and all others at 30° C.

Using a Bel-Art 96-well replicating tool (Bel-Art Products) the cultures were then spotted undiluted or as a 1:10 dilution (diluted in SCD-Ura) onto fresh 15 cm plates containing YPD solid medium (for 1 L of medium, 20 g Bacto Peptone, 10 g Bacto Yeast Extract and 15 g Bacto Agar are combined, and after autoclaving 20 g glucose are added as a sterile 20% solution). Approximately 3 μl from each well was deposited onto the recipient plate. The spots were allowed to dry and the plates were incubated at 30° C. for 1 day to allow surviving cells to grow into cell spots or individual colonies. The cell density of each transformant for each selective condition was scored on a relative scale from 0-3; 0 being no growth, 1 slight growth, 2 significant growth, and 3 confluent growth. Both the undiluted and diluted spots were taken into account to generate the score. To obtain a final activity score for each fusion polynucleotide TEF1 centromeric plasmid under each selective condition, the quadruplicate scores for each selective condition obtained for the control plasmid were summed and then subtracted from the sum of the scores obtained with the fusion polynucleotide TEF1 centromeric plasmids. Final activity scores below zero were scored as zero. A cumulative score was calculated by adding the individual activity scores for each fusion polynucleotide TEF1 centromeric plasmid. All scores are shown in Table 3 under the columns labeled ‘Activity scores’.

Yeast strain BY4741 transformed with the set of 63 fusion polynucleotide TEF1 centromeric plasmids showed significant resistance to or tolerance of elevated temperature, ethanol, butanol, and/or low pH compared to the negative control plasmid p466-TEF1, as shown in Table 3 below.

Activity scores above background of the 63 fusion polynucleotide TEF1 centromeric plasmids are shown in Table 3 below.

TABLE 3 Resistance and tolerance activities of 63 fusion polynucleotides in glucose-containing rich medium in S. cerevisiae Fusion poly- Fusion nucleotide poly- Activity scores Fusion nucleic nucleotide pH 3 poly- acid protein (0.1M Cumu- nucleotide SEQ SEQ Heat Ethanol Butanol sodium lative name ID ID (42° C.) (15%) (3%) acetate) score Y1-5A 1 64 1.5 4.5 3.0 6.0 15.0 Y1-7A 2 65 0.0 2.0 1.0 4.0 7.0 Y1-9A 3 66 0.0 0.0 0.0 0.0 0.0 Y1-13A 4 67 1.0 5.0 3.0 6.0 15.0 Y1-17A 5 68 0.0 3.0 1.0 4.0 8.0 Y1-18A 6 69 0.0 0.0 0.0 0.0 0.0 Y1-19A 7 70 2.0 4.0 3.0 6.0 15.0 Y1-20A 8 71 0.0 4.0 1.0 5.0 10.0 Y1-21A 9 72 0.0 1.0 1.0 2.0 4.0 Y1-23A 10 73 0.0 2.0 0.0 4.0 6.0 Y1-25A 11 74 0.0 0.0 0.0 0.0 0.0 Y1-28A 12 75 0.0 4.0 1.5 6.0 11.5 Y1-33A 13 76 0.0 0.0 0.0 0.5 0.5 Y1-34B 14 77 1.0 4.0 1.5 5.5 12.0 Y1-38A 15 78 1.0 4.0 1.0 6.0 12.0 Y1-39B 16 79 1.0 4.0 2.0 6.0 13.0 Y1-40A 17 80 1.0 4.0 2.0 6.0 13.0 Y1-43A 18 81 2.5 4.0 2.5 6.0 15.0 Y1-45A 19 82 0.0 2.0 1.0 4.0 7.0 Y1-47A 20 83 1.0 3.0 1.0 6.0 11.0 Y1-48A 21 84 0.0 3.0 1.0 6.0 10.0 Y1-49A 22 85 0.0 0.0 0.0 0.0 0.0 Y1-58B 23 86 0.0 0.0 0.0 0.5 0.5 Y1-58C 24 87 0.0 0.0 0.0 0.0 0.0 Y1-66 25 88 0.0 0.0 0.0 0.0 0.0 Y1-67B 26 89 0.0 0.0 0.0 0.0 0.0 Y2-28A 27 90 0.0 0.0 0.0 0.0 0.0 M21-A02 28 91 2.0 4.0 2.0 6.0 14.0 M21-A03 29 92 5.0 5.5 5.0 6.0 21.5 M21-A04 30 93 2.0 4.5 2.5 6.0 15.0 M21-A09 31 94 1.5 3.5 2.0 5.5 12.5 M21-C08 32 95 3.0 6.0 2.0 7.0 18.0 M21-D06 33 96 0.0 4.0 3.0 6.0 13.0 M22-C01 34 97 0.0 6.0 5.0 6.0 17.0 M22-C05 35 98 0.0 4.0 3.0 6.0 13.0 M22-D01 36 99 2.0 4.0 3.0 6.0 15.0 M23-C03 37 100 4.0 6.0 6.0 6.0 22.0 M23-D02 38 101 0.0 1.0 0.5 2.5 4.0 M23-D09 39 102 0.5 5.0 2.0 6.0 13.5 M23-E02 40 103 0.0 5.0 3.0 6.0 14.0 M23-F02 41 104 3.5 6.0 4.0 6.0 19.5 M23-H01 42 105 0.0 0.0 0.0 0.0 0.0 M24-A05 43 106 2.0 5.0 4.0 6.0 17.0 M24-B12 44 107 0.5 4.0 3.5 6.0 14.0 M24-D11 45 108 0.0 0.0 0.0 0.0 0.0 M24-E05 46 109 0.0 3.0 3.0 4.0 10.0 M24-F06 47 110 2.0 6.0 5.0 6.0 19.0 M25-E01 48 111 0.0 3.0 1.0 4.0 8.0 M25-F04 49 112 0.0 4.0 2.0 6.0 12.0 M25-G08 50 113 0.0 4.0 3.0 6.0 13.0 M25-G10 51 114 0.0 1.0 0.0 2.0 3.0 M25-H11 52 115 0.0 1.5 0.0 3.0 4.5 M26-A12 53 116 0.0 0.0 0.0 0.0 0.0 M26-D06 54 117 0.0 4.0 2.0 6.0 12.0 M27-A01 55 118 0.5 2.0 2.0 4.0 8.5 M27-B07 56 119 0.5 5.5 4.5 6.0 16.5 M27-F08 57 120 0.0 0.0 0.0 0.0 0.0 M28-A04 58 121 0.0 0.0 0.0 0.0 0.0 M28-C09 59 122 0.0 0.0 0.0 0.0 0.0 M28-D06 60 123 0.0 3.0 3.0 5.5 11.5 M28-E04 61 124 0.0 3.0 3.5 5.0 11.5 M29-E07 62 125 0.5 6.0 5.0 6.0 17.5 M30-E11 63 126 0.0 0.0 1.0 0.0 1.0 p466-TEF1 — — 0.0 0.0 0.0 0.0 0.0

Example 4: Quantitative Resistance and Tolerance Phenotypes in Galactose-Containing Media of Yeast Strains Transformed with Fusion Polynucleotide Centromeric Plasmids

Eighteen (18) selected fusion polynucleotide GAL1 centromeric plasmids from Example 2 were used to generate quantitative measurements of ethanol and butanol resistance and tolerance activity.

All experiments measuring tolerance and resistance activities were performed by using strain BY4741 (Brachmann 1998) transformed with each fusion polynucleotide GAL1 centromeric plasmid. Yeast transformations were performed using the lithium acetate-heat shock method as described in Example 2. Four independent transformants of each fusion polynucleotide GAL1 centromeric plasmid were tested. The individual fusion polynucleotide GAL1 centromeric plasmid transformants of strain BY4741 were maintained on minimal uracil dropout solid medium containing glucose as a carbon source (SCD-Ura agar; for 1 L medium, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix, and 15 g Bacto Agar are combined, the pH is adjusted to 5.6-5.8 with 120 μl 1 ON NaOH and after autoclaving 20 g of glucose are added as a sterile 20% solution).

Yeast strains transformed with the 18 fusion polynucleotide GAL1 centromeric plasmids, as well as the p416-GAL1 control plasmid, were tested for resistance and tolerance to ethanol and butanol in minimal media containing raffinose and galactose as carbon sources. The strains were first grown in 96-well plates (2 ml square wells) containing minimal uracil dropout medium containing 2% raffinose as a carbon source (SCRaf-Ura: for 1 L of medium, 6.7 g yeast nitrogen base and 0.77 g uracil dropout mix are combined, the pH is adjusted to 5.6-5.8 by the addition of 120 μl 10N NaOH and after autoclaving 20 g raffinose are added as a sterile 20% solution). Cells were incubated for 16 hours at 30° C. with constant shaking at 800 rpm.

The cell densities were then measured with a hemocytometer, and the cell suspensions diluted to a final cell density of 1×10⁷ cells/ml in 1.25 rich medium containing raffinose and galactose as carbon sources (YPRaf-Gal; for 1 L of medium: 20 g Bacto Peptone and 10 g Bacto Yeast Extract are combined, and after autoclaving 20 g of raffinose and 20 g of galactose are added as sterile 20% solutions). Cells were cultured for an additional 4 hours at 30° C. with constant shaking at 800 rpm.

The cell suspensions were then added in 0.25 ml aliquots to fresh 96-well plates (2 ml square wells) and combined with 0.25 ml per well of fresh YPRaf-Gal containing a 2× concentration of one selective agent. The selective agents used were: ethanol at a final concentration of 15% and n-butanol at a final concentration of 3%. All selective cultures were incubated for 2 days at 30° C. with constant shaking at 800 rpm.

The cultures were then diluted 1:10 and 1:100 in minimal uracil dropout medium containing glucose as a carbon source (SCD-Ura; for 1 L medium, 6.7 g yeast nitrogen base and 0.77 g uracil dropout mix are combined, the pH is adjusted to 5.6-5.8 by the addition of 120 μl 10N NaOH and after autoclaving 20 g of glucose are added as a sterile 20% solution). 100 μl aliquots of the undiluted and diluted cells were plated onto 10 cm plates containing solid minimal uracil dropout medium containing glucose as a carbon source (SCD-Ura agar; for 1 L medium, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix and 20 g Bacto Peptone are combined, the pH is adjusted to 5.6-5.8 by the addition of 120 μl 10N NaOH and after autoclaving 20 g of glucose are added as a sterile 20% solution). The plates were allowed to dry and were incubated at 30° C. for 2 days to allow surviving cells to grow into colonies. Colonies were counted on each plate, and the average number of surviving cells and the standard deviation (Std Dev) for each set of transformants were computed. The results are shown in Table 4 under the column labeled ‘Number of surviving cells’. The number of starting cells in each culture was approximately 2.5×10⁶.

From the numbers of surviving cells shown in Table 4 it is clear that yeast strain BY4741 transformed with the 18 fusion polynucleotide GAL1 centromeric plasmids showed significant resistance to or tolerance of ethanol and butanol, compared to the negative control plasmid p466-GAL1.

All surviving cell numbers are listed in Table 4 below.

TABLE 4 Butanol and ethanol resistance and tolerance activities of 18 fusion polynucleotides in galactose-containing rich medium in S. cerevisiae Fusion poly- Fusion Fusion nucleotide poly- poly- nucleic nucleotide Number of surving cells nucleotide acid protein 3% Butanol 15% ethanol name SEQ ID SEQ ID Mean Std Dev. Mean Std Dev. Y1-9A 3 66 3,525 222 52,500 6,245 Y1-17A 5 68 9,600 294 165,500 21,315 Y1-20A 8 71 14,925 704 100,500 8,426 Y1-21A 9 72 4,550 289 4,475 834 Y1-23A 10 73 8,525 457 16,025 1,090 Y1-28A 12 75 7,400 455 26,400 7,189 Y1-33A 13 76 1,900 392 9,575 1,962 Y1-34B 14 77 19,300 883 17,025 954 Y1-48A 21 84 7,800 440 17,425 2,645 Y1-66C 25 88 1,875 330 18,675 2,012 M21-A09 31 94 17,500 606 28,700 2,706 M23-D02 38 101 1,575 403 15,100 1,158 M23-H01 42 105 2,350 129 650 129 M24-E05 46 109 9,225 1,195 14,725 1,480 M25-E01 48 111 12,550 480 60,250 17,727 M26-A12 53 116 188,750 7,890 382,750 20,982 M26-D06 54 117 13,625 377 7,650 1,287 M27-A01 55 118 19,250 656 21,625 1,834 p416-GAL1 127 — 375 126 575 222

Example 5: Comparison of Resistance and Tolerance Phenotypes Conferred by Fusion Polynucleotides and Individual ORFs in Glucose-Containing Medium

Nineteen (19) selected fusion polynucleotide TEF1 centromeric plasmids from example 3 were used to generate quantitative measurements of heat, ethanol, butanol and low pH resistance and tolerance activity. The 19 fusion polynucleotides were compared in their activity to the 19 individual full length open reading frames (ORFs) that were the building blocks of the fusion polynucleotides.

The 19 fusion polynucleotides and the 19 individual ORFs were cloned into the yeast expression vector p466-TEF1 (SEQ. ID No 128). The yeast centromeric plasmid p466-TEF1 contains the following sequences for plasmid propagation in yeast and E. coli, and for expression of an inserted polynucleotide: the bacterial replicon of plasmid pMB1; the bacterial ampicillin-resistance gene; the yeast CEN6/ARSH4 cassette (Sikorski 1989) which contains the chromosome 6 centromere as well as the yeast histone H4-associated autonomously replicating sequence (ARS); the yeast URA3 prototrophic marker gene; and the yeast TEF1 promoter placed adjacent the CYC1 terminator in a manner that allows expression of coding regions placed between them (see SEQ ID NO:128). All polynucleotides were cloned between nucleotides 3029 and 3030 of SEQ ID NO 128. The 19 fusion polynucleotides cloned into p466-TEF1 are referred to as ‘fusion polynucleotide TEF1 centromeric plasmids’ and the 19 individual full length open reading frames cloned into p466-TEF1 are referred to as ‘individual ORF TEF1 centromeric plasmids’, and collectively as ‘TEF1 centromeric plasmids’ below.

All experiments measuring tolerance and resistance activities were performed using strain BY4741 (Brachmann 1998) that was transformed with each of the 19 fusion polynucleotide TEF1 centromeric plasmids and the 19 individual ORF TEF1 centromeric plasmids, as well as the p466-TEF1 control vector. Yeast transformations were performed using the lithium acetate-heat shock method as described in Example 2. Four independent transformants of each TEF1 centromeric plasmid were tested. The BY4741 transformants were maintained on minimal uracil dropout solid medium containing glucose as a carbon source (SCD-Ura agar; for 1 L medium, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix, and 15 g Bacto Agar are combined, the pH is adjusted to 5.6-5.8 with 120 μl 10N NaOH and after autoclaving 20 g of glucose are added as a sterile 20% solution).

Resistance and tolerance of the 39 transformed yeast strains to heat (42° C.), ethanol (15%), butanol (3%) and low pH (pH 3.0 in 0.2M sodium acetate) were measured in quadruplicate by testing four independent transformants of each construct. The 39 strains were first cultured in 96-well plates (2 ml square wells) in 1 ml per well of synthetic complete uracil dropout medium containing glucose as a carbon source (SCD-Ura; for 1 L medium, 6.7 g yeast nitrogen base, and 0.77 g uracil dropout mix are combined, the pH is adjusted to 5.6-5.8 by the addition of 120 μl 10N NaOH and after autoclaving 20 g of glucose are added as a sterile 20% solution). Cells were incubated for 16 hours at 30° C. shaking at 800 rpm with a 3 mm radius of gyration.

The cell densities were measured with a hemocytometer, the cell suspensions diluted in a fresh 96-well plate (2 ml square wells) to a final cell density of 1×10⁷ cells/ml in 1.25 ml SCD-Ura, and then grown for an additional 2 hours. The cell suspensions were then added in 0.25 ml aliquots to fresh 96-well plates (2 ml square wells) and combined with 0.25 ml per well of fresh SCD-Ura medium containing 2× concentration of one selective agent. The selective agents used were: ethanol at a final concentration of 15%, n-butanol at a final concentration of 3%, or sodium acetate pH3.0 at a final concentration of 0.2M. The sodium acetate was prepared as a 1M solution of sodium acetate pH 3.0 by mixing 2.74 ml glacial acetic acid with 0.11 g anhydrous sodium acetate in a final volume of 50 ml and filter sterilized using a 0.2 micron filter. For measuring heat tolerance, the 0.25 ml aliquots of cell suspension were combined with 0.25 ml of SCD-Ura medium and cultured in 96-well plates (2 ml square wells) at 42° C. All selective cultures were cultured for 48 hours with constant shaking at 800 rpm; those measuring heat tolerance were incubated at 42° C. and all others at 30° C.

The cultures were then diluted 1:100 and 1:500 in SCD-Ura. 150 μl aliquots of the diluted cells were plated onto 10 cm plates containing solid minimal uracil dropout medium containing glucose as a carbon source (SCD-Ura agar; for 1 L medium, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix, and 15 g Bacto Agar are combined, the pH is adjusted to 5.6-5.8 using 120 μl 10N NaOH, and after autoclaving 20 g glucose are added as a sterile 20% solution). The plates were allowed to dry and were incubated at 30° C. for 2 days to allow surviving cells to grow into colonies. Colonies were counted on each plate, and the average number of surviving cells and the standard deviations (Std Dev) from each set of transformants computed. Results are shown in Table 5 (FIGS. 1 and 2) under the columns labeled ‘Number of surviving cells’. The number of starting cells in each culture was approximately 2.5×10⁶.

Yeast strain BY4741 transformed with various fusion polynucleotide TEF1 centromeric plasmids showed enhanced resistance to or tolerance of heat, ethanol, butanol and low pH, compared to the individual ORF TEF1 centromeric plasmids, as shown in Table 5. Yeast strain BY4741 containing the negative control plasmid p466-TEF1 (SEQ ID NO 128) served as a control.

Only one of the individual ORFs (WHI2) showed any stress tolerance activity; all the others had no measurable activity. Activities of the fusion polynucleotides that surpass the individual WHI2 ORF score are identified by grey shaded cells in Table 5 (FIGS. 1 and 2). In many cases, the activity level is significantly above that of the individual WHI2 ORF, suggesting unexpected gain-of-function activity by the fusion polynucleotides.

All resistance and tolerance scores are listed in Table 5 which is split into two parts; part A (FIG. 1) shows cell counts from heat and ethanol selections and part B (FIG. 2) shows cell counts from butanol and low pH selections.

Example 6: Comparison of Resistance and Tolerance Phenotypes Conferred by KEOPS/EGO Fusion Polynucleotides and Individual ORFs in Glucose-Containing Medium

Examples 2, 3 and 5 contain evidence that members of the yeast KEOPS and EGO protein complexes, when fused with the yeast WHI2 ORF, result in elevated levels of stress and alcohol tolerance in yeast strains expressing these fusion proteins (see data for fusion polynucleotides Y1-38A, M22-C05, M23-C03, M27-B07, and M21-008 in Tables 2, 3, and 5.

Both the KEOPS complex and the EGO complex contain 5 different proteins. The members of the KEOPS complex are named BUD32, GON7, KAE1, PCC1 and CGI121. The members of the EGO complex are named SLM4, LTV1, MEH1, GTR1 and GTR2.

To test whether all members of the KEOPS and EGO complexes are able to confer stress and alcohol tolerance when fused with WHI2, 20 new fusions were constructed that combined all 10 members of the two complexes with WHI2 in both orientations. That is, each complex member was present in the fusion polypeptide in the 5′ position relative to WHI2 as well as in the 3′ position. The 20 resulting fusion polynucleotides (PP0219-PP0238; SEQ ID NOs 205-224, respectively, whose protein sequences are given in SEQ ID NOs 225-244, respectively) were cloned into the yeast expression vector p466-TEF1 (SEQ. ID No 128); see example 3 for details. The resulting 20 new fusion polynucleotide constructs are referred to as the ‘KEOPS/EGO TEF1 fusion polynucleotide centromeric plasmids’. Each of the 11 full-length ORFs (BUD32, GON7, KAE1, PCC1, CGI121, SLM4, LTV1, MEH1, GTR1, GTR2 and WHI2) were also individually cloned into yeast expression vector p466-TEF1 (SEQ. ID No 128); see example 3 for details. The resulting 11 new individual full length ORF constructs are referred to as the ‘KEOPS/EGO TEF1 individual ORF centromeric plasmids’. All centromeric expression constructs discussed in this example are collectively referred to as ‘TEF1 centromeric plasmids’.

The 20 KEOPS/EGO TEF1 fusion polynucleotide centromeric plasmids and the 11 KEOPS/EGO TEF1 individual ORF centromeric plasmids were used to generate quantitative measurements of heat, ethanol, butanol and low pH resistance/tolerance activity. The 20 fusion polynucleotides were compared in their activity to the 11 individual ORFs that are the building blocks of the 20 fusion polynucleotides.

All experiments measuring tolerance and resistance activities were performed using strain BY4741 (Brachmann 1998) transformed with each of the 20 KEOPS/EGO TEF1 fusion polynucleotide centromeric plasmids and the 11 KEOPS/EGO TEF1 individual ORF centromeric plasmids, as well as the p466-TEF1 control vector. Yeast transformations were performed using the lithium acetate-heat shock method as described in Example 2. Four independent transformants of each TEF1 centromeric plasmid were tested. The BY4741 transformants were maintained on minimal uracil dropout solid medium containing glucose as a carbon source (SCD-Ura agar; for 1 L medium, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix, and 15 g Bacto Agar are combined, the pH is adjusted to 5.6-5.8 with 120 μl 10N NaOH and after autoclaving 20 g of glucose are added as a sterile 20% solution).

Resistance and tolerance of the 32 yeast strains (BY4741 transformed with 20 KEOPS/EGO TEF1 fusion polynucleotide centromeric plasmids, 11 KEOPS/EGO TEF1 individual ORF centromeric plasmids and one control vector) to heat (42° C.), ethanol (15%), butanol (3%) and low pH (pH 3.0 in 0.2M sodium acetate) were measured in quadruplicate by testing four independent transformants of each construct. The 32 strains were first cultured in 96-well plates (2 ml square wells) in 1 ml per well of synthetic complete uracil dropout medium containing glucose as a carbon source (SCD-Ura; for 1 L medium, 6.7 g yeast nitrogen base and 0.77 g uracil dropout mix are combined, the pH is adjusted to 5.6-5.8 with 120 μl 10N NaOH, and after autoclaving 20 g of glucose are added as a sterile 20% solution). The cells were incubated for 16 hours at 30° C. with constant shaking at 800 rpm with a 3 mm radius of gyration.

The cell densities were measured with a hemocytometer, the cell suspensions diluted in a fresh 96-well plate (2 ml square wells) to a final cell density of 1×10⁷ cells/ml in 1.25 ml SCD-Ura, and then grown for an additional 2 hours. The cell suspensions were added in 0.25 ml aliquots to fresh 96-well plates (2 ml square wells) and combined with 0.25 ml per well of fresh SCD-Ura medium containing a 2× concentration of one selective agent. The selective agents used were: ethanol at a final concentration of 15%; n-butanol at a final concentration of n-butanol or sodium acetate pH3.0 at a final concentration of 0.2M. The sodium acetate was prepared as a 1M solution of sodium acetate pH 3.0 by mixing 2.74 ml glacial acetic acid with 0.11 g anhydrous sodium acetate in 50 ml final volume and filter sterilized using a 0.2 micron filter. For measuring heat tolerance, the 0.25 ml aliquots of cell suspension were combined with 0.25 ml of SCD-Ura medium and incubated in 96-well plates (2 ml square wells) at 42° C. All selective cultures were incubated for 72 hours: those measuring heat tolerance at 42° C. and all others at 30° C., with the exception of the butanol selections which were cultured for 48 hours. All selective cultures were incubated with constant shaking at 800 rpm.

The cultures were then diluted 1:100 and 1:500 in SCD-Ura. 150 μl aliquots of the diluted cells were plated onto 10 cm plates containing solid minimal uracil dropout medium containing glucose as a carbon source (SCD-Ura agar; for 1 L medium, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix and 15 g Bacto Agar are combined, the pH is adjusted to 5.6-5.8 with 120 μl 10N NaOH, and after autoclaving 20 g of glucose are added as a sterile 20% solution). The plates were allowed to dry and were incubated at 30° C. for 2 days to allow surviving cells to grow into colonies. Colonies were counted on each plate, and the average number of surviving cells and their standard deviations (Std Dev) from each set of transformants were computed. Results are shown in Table 6 (FIGS. 3 and 4) under the columns labeled ‘Number of surviving cells’. The number of starting cells in each culture was approximately 2.5×10⁶.

Yeast strain BY4741 transformed with various KEOPS/EGO TEF1 fusion polynucleotide centromeric plasmids showed enhanced resistance to or tolerance of heat, ethanol, butanol and low pH, compared to the KEOPS/EGO TEF1 individual ORF centromeric plasmids, as shown in Table 6 (FIGS. 3 and 4). Yeast strain BY4741 containing the negative control plasmid p466-TEF1 (SEQ ID NO 128) served as a control.

Only one of the individual full length ORFs (WHI2) showed any stress tolerance activity and all the others had no measurable activity. Activities of the fusion polynucleotides that surpass the WHI2 score are identified by grey shaded cells in Table 6 (FIGS. 3 and 4). In many cases, the activity level is significantly above that of the individual full length WHI2 ORF, suggesting unexpected gain-of-function activity by the fusion polynucleotide. Furthermore, the table shows that each component of the KEOPS complex, and each component of the EGO complex, led to enhanced activity of WHI2 in at least one fusion polynucleotide and phenotypic measurement, suggesting that all members of one complex are able to interact positively with the activity of WHI2 in a fusion protein and/or cause unexpected gain-of-function tolerance or resistance activity when fused with WHI2.

All resistance and tolerance scores are listed in Table 6 which is split into two parts; part A (FIG. 3) shows cell counts from heat and ethanol selections and part B (FIG. 4) shows cell counts from the butanol and low pH selections.

Example 7: Comparison of Resistance and Tolerance Phenotypes Conferred by Fusion Polynucleotides and Individual ORFs in Galactose-Containing Medium

Fourteen selected fusion polynucleotide GAL1 centromeric plasmids from Example 2 were used to generate quantitative measurements for heat, ethanol, butanol and low pH resistance and/or tolerance activity. The 14 fusion polynucleotides were compared in their activity to the 14 individual full length ORFs that are the building blocks of the fusion polynucleotides.

The 14 fusion polynucleotides and the 14 individual ORFs were cloned into a derivative of the yeast centromeric plasmid p416-GAL1 (Mumberg 1995, Funk 2002). The yeast centromeric plasmid p416-GAL1 contains the following sequences for plasmid propagation in yeast and E. coli, and expression of an inserted polynucleotide: the bacterial replicon of plasmid pMB1; the bacterial ampicillin-resistance gene; the yeast CEN6/ARSH4 cassette (Sikorski 1989) containing the chromosome 6 centromere and the yeast histone H4-associated autonomously replicating sequence (ARS); the yeast URA3 prototrophic marker gene; and the yeast GAL1 promoter placed adjacent to the CYC1 terminator in a manner that allows expression of coding regions placed between them (see SEQ ID NO: 127). All polynucleotides were cloned between nucleotides 3206 and 3207 of SEQ ID NO 127.

The resulting set of centromeric plasmids containing expression cassettes of the 14 fusion polynucleotides are hereafter referred to as the ‘fusion polynucleotide GAL1 centromeric plasmids;’ the centromeric plasmids containing expression cassettes of the 14 individual ORFs are hereafter referred to as the ‘individual ORF GAL1 centromeric plasmids’. Collectively, the expression constructs are referred to as the ‘GAL1 centromeric plasmids’.

All experiments measuring tolerance and resistance activities of the GAL1 centromeric plasmids were performed using strain BY4741 (Brachmann 1998) transformed with each GAL1 centromeric plasmid. Yeast transformations were performed using the lithium acetate-heat shock method as described in Example 2. The GAL1 centromeric plasmid transformants of strain BY4741 were maintained on minimal uracil dropout solid medium containing glucose as a carbon source (SCD-Ura agar; for 1 L medium, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix, and 15 g Bacto Agar are combined, the pH is adjusted to 5.6-5.8 with 120 μl 10N NaOH and after autoclaving 20 g of glucose are added as a sterile 20% solution).

Resistance and/or tolerance phenotypes for heat (42° C.), ethanol (15%), butanol (3%), low pH (pH 3.0 in 0.2M sodium acetate) and salt (2M NaCl) were measured in triplicate for the 12 yeast strains shown in Table 7A (FIG. 5) with three independent transformants of yeast strain BY4741 with each GAL1 centromeric plasmid. The 13 strains were first cultured in 96-well plates (2 ml square wells) in synthetic complete uracil dropout medium containing glucose as a carbon source (SCD-Ura; for 1 L medium, 6.7 g yeast nitrogen base and 0.77 g uracil dropout mix are combined, the pH is adjusted to 5.6-5.8 with 120 μl 10N NaOH, and after autoclaving 20 g of glucose are added as a sterile 20% solution). Cells were incubated for 16 hours at 30° C. with constant shaking at 800 rpm with a 3 mm radius of gyration.

The cell densities were measured with a hemocytometer and the cell suspensions diluted to a final cell density of 1×10⁷ cells/ml in 1.25 ml rich medium containing galactose as a carbon source (YPGal; for 1 L medium, 20 g Bacto Peptone and 10 g Bacto Yeast Extract are combined and after autoclaving 20 g of galactose are added as a sterile 20% solution). The diluted cultures were incubated for an additional 5 hours under the same conditions. The cell suspensions were then added in 0.25 ml aliquots to fresh 96-well plates (2 ml square wells) and combined with 0.25 ml per well of fresh YPGal containing a 2× concentration of one selective agent. The selective agents used were: NaCl at a final concentration of 2M (salt selection); ethanol at a final concentration of 15%; n-butanol at a final concentration of 3%; or sodium acetate pH 3.0 at a final concentration of 0.2M. The sodium acetate was prepared as a 1M solution of sodium acetate pH 3.0 by mixing 2.74 ml glacial acetic acid with 0.11 g anhydrous sodium acetate in 50 ml final volume and filter sterilized using a 0.2 micron filter. For measuring heat tolerance, the 0.25 ml aliquots of cell suspension were combined with 0.25 ml of YPGal and cultured in 96-well plates (2 ml square wells) at 42° C. All selective cultures were incubated for 3 days with constant shaking at 800 rpm; those measuring heat tolerance at 42° C. and all others at 30° C.

The cultures for Table 7A (FIG. 5) were then spotted undiluted or in 1:10 dilutions (diluted in SCD-Ura) onto fresh 15 cm plates containing solid rich medium with glucose as a carbon source (YPD agar; for 1 L medium, 20 g Bacto Peptone, 10 g Bacto Yeast Extract and 15 g Bacto Agar are combined, and after autoclaving 20 g glucose are added as a 20% sterile solution). The spotting was done using a Bel-Art 96-well replicating tool (Bel-Art Products) that deposits spots of approximately 3 μl from each well onto the recipient plate. The spots were allowed to dry, the plates incubated at 30° C. for 1 day to allow surviving cells to grow into cell spots or individual colonies, and the cell density of each transformant for each selective condition scored on a relative scale from 0-3; 0 being no growth, 1 slight growth, 2 significant growth and 3 confluent growth. Both the undiluted and diluted spots were taken into account to generate the score. To obtain a final activity score for each fusion polynucleotide GAL1 centromeric plasmid and each selective condition, the triplicate scores for each selective condition were added, and the added triplicate score obtained with the control plasmid subtracted, and the result divided by the number of replicates (3). Final activity scores below zero were scored as zero. All scores are shown in Table 7A (FIG. 5) under the columns labeled ‘Activity scores’.

Resistance and tolerance phenotypes of the 20 yeast strains shown in Table 7B (FIG. 6) to heat (42° C.), ethanol (15%), butanol (3%), low pH (pH 3.0 in 0.2M sodium acetate) and salt (2M NaCl) were measured in quadruplicate with four independent transformants of yeast strain BY4741 with each GAL1 centromeric plasmid. The strains were first grown in 96-well plates (2 ml square wells) containing minimal uracil dropout medium containing 2% raffinose as a carbon source (SCRaf-Ura; for 1 L medium, 6.7 g yeast nitrogen base and 0.77 g uracil dropout mix are combined, pH is adjusted to 5.6-5.8 with 120 μl 10N NaOH, and after autoclaving 20 g of raffinose are added as a sterile 20% solution). Cells were incubated for 16 hours at 30° C. with constant shaking at 800 rpm on a microshaker with a 3 mm radius of gyration.

The cell densities were then measured with a hemocytometer, and the cell suspensions diluted to a final cell density of 1×10⁷ cells/ml in 1.25 rich medium containing raffinose and galactose as carbon sources (YPRaf-Gal; for 1 L medium, 20 g Bacto Peptone and 10 g Bacto Yeast Extract are combined and after autoclaving 20 g of raffinose and 20 g of galactose are added as sterile 20% solutions). The cell suspensions to fresh 96-well plates (2 ml square wells) and cultured for an additional 2 hours in the same manner. The cultures were then were then added in 0.25 ml aliquots to fresh 96-well plates (2 ml square wells) containing 0.25 ml per well of YPRaf-Gal with 2× concentration of one selective agent. The selective agents used were 15% final concentration of ethanol, 3% final concentration of n-butanol, 0.2M final concentration of sodium acetate pH 3.0 or 2M final concentration of NaCl, The sodium acetate was prepared as a 1M solution of sodium acetate pH 3.0 by mixing 2.74 ml glacial acetic acid with 0.11 g anhydrous sodium acetate in 50 ml final volume and filter sterilized using a 0.2 micron filter For measuring heat tolerance, the 0.25 ml aliquots of cell suspension were combined with 0.25 ml of YPRaf-Gal and cultured in 96-well plates (2 ml square wells) at 42° C. All selective cultures were incubated for 48 hours with constant shaking at 800 rpm; those measuring heat tolerance at 42° C. and all others at 30° C.

The cultures for Table 7B (FIG. 6) were then spotted undiluted or in 1:10 dilutions (diluted in SCD-Ura) onto fresh 15 cm plates containing solid rich medium with glucose as a carbon source (YPD agar; for 1 L medium, 20 g Bacto Peptone, 10 g Bacto Yeast Extract and 15 g Bacto Agar are combined, and after autoclaving 20 g glucose are added as a sterile 20% solution). The cultures were spotted using a Bel-Art Products Bel-Art 96-well replicating tool that deposits spots of approximately 3 μl from each well onto the recipient plate. The spots were allowed to dry, the plates incubated at 30° C. for 1 day to allow surviving cells to grow into cell spots or individual colonies, and the cell density of each transformant for each selective condition scored on a relative scale from 0-3; 0 being no growth, 1 slight growth, 2 significant growth and 3 confluent growth. Both the undiluted and diluted spots were taken into account to generate the score. To obtain a final activity score for each fusion polynucleotide GAL1 centromeric plasmid for each selective condition, the quadruplicate scores for each selective condition were added, and the added score obtained with the control plasmid subtracted, and the result divided by the number of replicates (4). Final activity scores below zero were scored as zero. All scores are shown in Table 7B (FIG. 6) under the columns labeled ‘Activity scores’.

Yeast strain BY4741 transformed with the fusion polynucleotide GAL1 centromeric plasmids showed enhanced resistance to or tolerance of heat, ethanol, butanol, low pH and/or salt, compared to the individual ORF GAL1 centromeric plasmids, as shown in Table 7 (FIGS. 5 and 6). Yeast strain BY4741 containing the negative control plasmid p416-GAL1 (Mumberg 1995, Funk 2002) served as a control.

From the stress tolerance activities of the individual ORFs composing each fusion polynucleotide, the maximal expected stress tolerance score for each fusion polynucleotide can easily be calculated by adding the individual stress tolerance scores of each ORF contained in the fusion polynucleotide. Activities of the fusion polynucleotides that surpass this additive score are identified by grey shaded cells in Table 7 (FIGS. 5 and 6). The activity of the fusion polynucleotide would be expected to be equivalent to the individual value of one of the component ORFs and perhaps, in exceptional cases, to approach the additive score of the two component ORFs. However, the table shows that many of the fusion polynucleotide activities are even higher than the additive values. Fusion polynucleotide activity surpassed the additive activity levels in 19 out of 30 cases in Table 7A (FIG. 5) and 24 out of 45 cases in Table 7B (FIG. 6).

In one or more of the phenotypic categories (heat, ethanol, butanol, low pH and salt tolerance), each fusion polynucleotide listed in Table 7 (FIGS. 5 and 6) shows unexpected gain-of-function activity that is created by fusing together the two component ORFs. However, the expectation would have been that the activity of each fusion polynucleotide approximates the activity of one of the starting ORFs, or at best matches the additive activities of the two ORFs.

Activity scores of 14 fusion polynucleotide GAL1 centromeric plasmids and their 14 individual component ORFs are shown in Table 7 (FIGS. 5 and 6).

Example 8: Resistance and Tolerance Phenotypes in Glucose-Containing Media of Yeast Strains Transformed with Fusion Polynucleotide Centromeric Plasmids

All 83 fusion polynucleotides (SEQ ID NOs 1-63 and 205-224) are cloned into the yeast expression vector p466-TEF1 (SEQ. ID No 128) which is similar to the yeast centromeric plasmid p416-TEF1 (Mumberg 1995, Funk 2002). The yeast centromeric plasmid p466-TEF1 contains the following sequences for plasmid propagation in yeast and E. coli, and expression of an inserted polynucleotide: the bacterial replicon of plasmid pMB1; the bacterial ampicillin-resistance gene; the yeast CEN6/ARSH4 cassette (Sikorski 1989) containing the chromosome 6 centromere and the yeast histone H4-associated autonomously replicating sequence (ARS); the yeast URA3 prototrophic marker gene; and the yeast TEF1 promoter placed adjacent to the CYC1 terminator in a manner that allows expression of coding regions inserted between them. The sequence of this p466-TEF1 expression vector is given in SEQ ID NO 128. All polynucleotides are cloned between nucleotide numbers 3029 and 3030 of SEQ ID NO 128.

The resulting set of constructs, referred to as ‘fusion polynucleotide TEF1 centromeric plasmids’, contain expression cassettes of the 83 fusion polynucleotides that are given in SEQ ID NOs: 1-63, and 205-224 under control of the S. cerevisiae TEF1 promoter. These constructs are used for quantitative determinations of yeast tolerance to the following stresses and toxic agents: alcohols (propanol, isopropanol, iso-butanol, pentanol, hexanol, heptanol, octanol, nonanol, decanol, undecanol and dodecanol), alkanes (butane, pentane, hexane, heptane, octane, nonane, decane, undecane, dodecane, hexadecane), heavy metal ions (various ions of the elements Ag, silver; As, arsenic; Cd, cadmium; Cr, chromium; Co, cobalt; Cu, copper; Hg, mercury; Ni, nickel; Pb, lead; Pt, platinum; Sb, antimony; Se, selenium; Tl, thallium; or Zn, zinc), oxidizing agents (hydrogen peroxide and other inorganic peroxides; inorganic oxidizing agents such as potassium permanganate; organic peroxides and hydroperoxides such as ethyl hydroperoxide, diacetyl peroxide, diethyl maleate, tert-butyl hydroperoxide, cumyl hydroperoxide and ascaridole; and other toxic compounds such as furfural, 5-hydroxymethylfurfural, benzoic acid derivatives (for example p-hydroxybenzoic acid), and other toxic lignin breakdown products found in sugar preparations derived from biomass (Luo 2002).

All experiments measuring tolerance and resistance activities of the fusion polynucleotides are performed using strain BY4741 (Brachmann 1998) transformed with each fusion polynucleotide TEF1 centromeric plasmid. Yeast transformations are performed using the lithium acetate-heat shock method as described in Example 2. The individual fusion polynucleotide TEF1 centromeric plasmid transformants of strain BY4741 are maintained on minimal uracil dropout solid medium containing glucose as a carbon source (SCD-Ura agar; for 1 L medium, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix, and 15 g Bacto Agar are combined, the pH is adjusted to 5.6-5.8 with 120 μl 10N NaOH and after autoclaving 20 g of glucose are added as a sterile 20% solution).

The tolerance determinations are performed either in rich medium containing glucose as a carbon source or in minimal medium containing glucose as a carbon source. The tolerance activities of each fusion polynucleotide TEF1 centromeric plasmid are measured in quadruplicate, with each of two independent transformants of each fusion polynucleotide TEF1 centromeric plasmid tested in duplicate.

Selective concentrations for all selective agents are determined by diluting an overnight culture of yeast strain BY4741 (Brachmann 1998) to a density of 5×10⁶ cells/ml in rich medium containing glucose as a carbon source (YPD; for 1 L medium, 20 g Bacto Peptone and 10 g Bacto Yeast Extract are combined and after autoclaving 20 g glucose are added as a 20% sterile solution) or minimal medium containing glucose as a carbon source (SCD-Ura; for 1 L medium, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix and 25 ml of 2 mg/ml uracil are combined, the pH is adjusted to 5.6-5.8 with 120 μl 10N NaOH and after autoclaving 20 g of glucose are added as a sterile 20% solution). The cells are pre-cultured by adding 0.25 ml of the cell suspension to each well of a 96-well plate (2 ml square wells) and incubating for 2 hours at 30° C. with constant shaking at 800 rpm with a 3 mm radius of gyration. To each well, 0.25 ml of the same fresh medium is then added containing different concentrations of the selective agents. Selective concentrations for alcohols range between 0.025% and 25% depending on alcohol chain length (Fujita 2004). Selective concentrations for alkanes range between 1% and 25% depending on alkane chain length (Gill 1972, Fujita 2004); selective concentrations for heavy metal ions range between 0.5 μM and 10 mM (Bitton 1984, Hsu 1992, Nguyen-nhu 2002, Soares 2003); selective concentrations for oxidizing agents range from 2-100 mM for hydrogen peroxide, other inorganic peroxides and potassium permanganate, and 0.5-10 mM for organic peroxides and hydroperoxides (Krems 1995, Nguyen-nhu 2002, Miyazaki 2005); selective concentrations for furfural, hydroxymethylfurfural and p-hydroxybenzoic acid range from 2-100 mM (Palmqvist 1999, Liu 2005, Liu 2006, Heer 2008, Liu 2008, Tofighi 2010). The selective plates are sealed and incubated at 30° C. shaking at 800 rpm with a 3 mm radius of gyration for 48-96 hours. The cell density of each culture is then measured with a hemocytometer, and the growth inhibitory concentration of each compound determined. Cells from each growth inhibited culture are then plated on fresh YPD solid medium (YPD agar; for 1 L medium, 20 g Bacto Peptone, 10 g Bacto Yeast Extract and 15 g Bacto Agar are combined and after autoclaving 20 g glucose are added as a 20% sterile solution) and allowed to grow for 1-2 days to assess the relative number of viable cells in each culture and to determine the lethal concentration of each compound. The compounds are then divided into lethal and growth-inhibitory, with separate tolerance and resistance assays conducted for each class.

For measurement of the resistance to and tolerance of lethal compounds among the alcohols, alkanes, heavy metal ions, oxidizing agents and other toxic compounds listed above, the 84 yeast strains (BY4741 transformed with 83 fusion polynucleotide TEF1 centromeric plasmids plus one control vector) are first cultured in 96-well plates (2 ml square wells) in 1 ml per well of SCD-Ura. Cells are incubated for 16 hours at 30° C. with constant shaking at 800 rpm with a 3 mm radius of gyration. The cell densities are then measured with a hemocytometer and the cells diluted in a fresh 96-well plate (2 ml square wells) to a final cell density of 1×10⁷ cells/ml in 1.25 ml SCD-Ura or YPD medium, and grown for an additional 2 hours. The cell suspensions are then added in 0.25 ml aliquots to fresh 96-well plates (2 ml square wells) and combined with 0.25 ml per well of fresh YPD medium or SCD-Ura medium, the freshly added medium containing 2× concentration of one selective agent. The selective agents used are listed above, and lethal concentrations of each are used in the selection. All selective cultures are cultured for 48-96 hours at 30° C. After the selection has been completed, the cultures are then diluted 1:10, 1:100 and 1:1000 in SCD-Ura liquid medium and 150 μl aliquots of the diluted cells are plated as ˜1 in spots onto 15 cm plates containing SCD-Ura agar medium or YPD agar medium. The plates are allowed to dry and are incubated at 30° C. for 2 days to allow surviving cells to grow into colonies. The colonies are counted, the multiple counts for each fusion polynucleotide TEF1 centromeric plasmid are averaged and standard deviations are calculated, to determine the relative stress tolerance and resistance phenotypes conferred by each fusion polynucleotide.

For measurement of the resistance to and tolerance of growth-inhibitory compounds among the alcohols, alkanes, heavy metal ions, oxidizing agents and other toxic compounds listed above, the 84 yeast strains (BY4741 transformed with 83 fusion polynucleotide TEF1 centromeric plasmid plus one control vector) are first cultured in 96-well plates (2 ml square wells) in 1 ml per well of SCD-Ura. Cells are incubated for 16 hours at 30° C. with constant shaking at 800 rpm with a 3 mm radius of gyration. The cell density is then measured with a hemocytometer, and the cells diluted in a fresh 96-well plate (2 ml square wells) to a final cell density of 1×10⁷ cells/ml in 1.25 ml SCD-Ura or YPD medium, and grown for an additional 2 hours. The cell suspensions are then added in 0.25 ml aliquots to fresh 96-well plates (2 ml square wells) and combined with 0.25 ml per well of fresh SCD-Ura or YPD medium, the freshly added medium containing 2× concentration of one selective agent. The selective agents used are listed above, and growth-inhibitory concentrations of each are used in the selection. All selective cultures are cultured for 48-96 hours at 30° C. After the selection has been completed, the cultures are diluted 1:100, 1:1000 and 1:10,000 in SCD-Ura liquid medium and 150 μl aliquots of the diluted cells are plated as ˜1 in spots onto 15 cm plates containing SCD-Ura agar medium or YPD agar medium. The plates are allowed to dry and are incubated at 30° C. for 2 days to allow surviving cells to grow into colonies. The colonies are counted, the multiple counts for each fusion polynucleotide TEF1 centromeric plasmid are averaged and used to calculate the number of viable cells in each culture as well as standard deviations, to determine the relative stress tolerance and resistance phenotypes conferred by each fusion polynucleotide.

Example 9: Efficient Method for Selection of Heat-Tolerant Yeast Clones

A collection or library of Saccharomyces cerevisiae in-frame fusion polynucleotides is prepared as described in U.S. patent application Ser. No. 14/134,619 and International Patent Application Serial Number PCT/US13/76526. The randomized in-frame fusion polynucleotides are cloned into a vector molecule, such the yeast expression vector p416-GAL1 (Funk 2002). The sequence of a p416-GAL1 derivative vector is given in SEQ ID NO 127 and contains the following sequences for plasmid propagation in yeast and E. coli and expression of an inserted polynucleotide: the bacterial replicon of plasmid pMB1, the bacterial ampicillin/carbenicillin-resistance gene, the yeast CEN6/ARSH4 cassette (Sikorski 1989) containing the chromosome 6 centromere and the yeast histone H4-associated autonomously replicating sequence (ARS), the yeast URA3 prototrophic marker gene, and the yeast GAL1 promoter and CYC1 terminator placed adjacent to each other in a manner that allows insertion of coding regions in between to allow their expression. All randomized in-frame fusion polynucleotides are cloned between nucleotide numbers 3206 and 3207 of SEQ ID NO 127.

Yeast transformations are performed by the lithium acetate-heat shock method (Gietz 2002, Gietz 2006, Gietz 2007). The yeast strain BY4741 (Brachmann 1998) from a plate or an overnight culture is inoculated into 50 ml of YPD medium (for 1 L medium, 20 g Bacto Peptone, 10 g Bacto Yeast Extract are combined and after autoclaving 20 g Glucose are added as a 20% sterile solution) at 30° C. on a shaker at 225 rpm from a starting density of 5×10⁶ cells/ml (cell density determined with a hemocytometer), and grown over several hours to a final cell density of 2×10⁷ cells/ml. The cells are harvested by centrifuging at 3000 g for 5 min, are then resuspended in 25 ml of sterile deionized water, and centrifuged again. Cells are resuspended in 1 ml of sterile water, transferred to a 1.5 ml microcentrifuge tube, centrifuged for 30 sec at 3000 rpm and the supernatant aspirated. The cell pellet is then resuspended in 0.4 ml of sterile deionized water. The cell suspension is combined with 3.26 ml of transformation mix (2.4 ml of 50% w/v PEG 3350, 360 μl 1M Lithium acetate and 500 μl 10 mg/ml sheared, boiled salmon sperm DNA) and mixed well. Aliquots of DNA (100 ng-1 μg) are pipetted into separate 1.5 ml microcentrifuge tubes and combined with 380 μl of the cell suspension in transformation mix. The cell/DNA mixture is mixed thoroughly and is incubated at 42° C. on a shaker at 250 rpm for 40 minutes. The transformations are then centrifuged for 1 minute at 3000 rpm in a microcentrifuge, the supernatant aspirated and each cell aliquot resuspended in 0.5-1 ml sterile deionized water. Depending on the desired density of colonies, 10 μl to 1 ml of the cell suspension are plated with sterile 4 mm glass beads onto one 10 cm or 15 cm plate containing synthetic complete uracil dropout solid medium having glucose as a carbon source (SCD-Ura agar; for 1 L, 6.7 g yeast nitrogen base, 0.77 g uracil dropout mix and 15 g Bacto agar are combined, the pH is adjusted with 120 μl 10N NaOH to bring the pH to 5.6-5.8, and after autoclaving 20 g glucose are added as a 20% sterile solution). After drying, the plates are covered and incubated at 30° C. for 3-4 days until colonies of transformants have formed.

After formation of colonies or lawns of cells transformed with randomized in-frame fusion polynucleotides, the transformed cells are removed from the selective plates by scraping with glass beads. This is done by adding to each 10 cm plate 5 ml synthetic complete uracil dropout medium with galactose as a carbon source (SCGal-Ura; for 1 L medium, 6.7 g yeast nitrogen base and 0.77 g uracil dropout mix are combined, the pH is adjusted with 120 μl 10N NaOH to bring the pH to 5.6-5.8 and, after autoclaving, 20 g galactose are added as a sterile 20% solution) together with 10×4 mm glass beads. Proportionally higher volumes of medium are added to larger plates. Using swirling and horizontal shaking motions to allow the glass beads to dislodge the yeast cells from the surface of the agar, the resuspended cells are collected with a pipet, using additional medium if desired to wash any remaining cells off the plate. Cells collected in this fashion are pelleted by centrifugation at 4000 rpm for 5 minutes. Cells are resuspended in SCGal-Ura at a cell density of 5×10⁶ cells/ml and cultured at 30° C. shaking at 250 rpm for 4-12 hours. This pre-culturing step allows induction of the GAL1 promoter used to express the randomized in-frame fusion polynucleotides.

For heat tolerance selection, tolerant cells are selected in liquid culture. The cell density in the suspension of yeast transformants containing in-frame fusion polynucleotides is determined with a hemocytometer, and the cells are suspended in SCGal-Ura at a cell density of 5×10⁶ cells/ml in 50 ml of medium in a 500 ml flask and cultured at 40-44° C. shaking at 250 rpm for 7 days. This selective culture is referred to as the ‘heat liquid selection culture’. Following the selection, 0.5 ml aliquots of the cell suspension are either plated directly on 15 cm SCD-Ura agar plates to select for surviving cells, or the cell suspension after selection is centrifuged at 3000 rpm for 5 minutes, the cell pellet suspended in 0.25 ml minimal uracil dropout solid medium with glucose as a carbon source (SCD-Ura; for 1 L, 6.7 g yeast nitrogen base and 0.77 g uracil dropout mix are combined, the pH is adjusted with 120 μl 10N NaOH to bring the pH to 5.6-5.8, and after autoclaving 20 g glucose are added as a 20% sterile solution) and plated on a 15 cm SCD-Ura agar plate. The plates are allowed to dry and incubated at 30° C. for 3-4 days until colonies have formed.

To boost the number of survivors from heat selection, it is advantageous to incubate the heat liquid selection culture at temperatures ranging from 4° C. to 25° C. either with or without shaking for 1-24 hours after removal from the heat selection. For example, following a heat selection at 42° C., the heat liquid selection culture is removed from the shaker in which the selection took place and transferred to room temperature where it is allowed to remain without shaking for 2 hours. The heat liquid selection culture is then incubated at 4° C. for 16 hours. The cells are then collected centrifuged at 3000 rpm for 5 minutes, the cell pellet suspended in 0.25 ml SCD-Ura and plated on a 15 cm SCD-Ura agar plate. The plate is allowed to dry and incubated at 30° C. for 3-4 days until colonies have formed. Comparison between the number of colonies formed when plating directly after heat selection, vs plating after successive incubation of the heat liquid selection culture at room temperature and 4° C. shows a greater number of colonies after successive incubation at room temperature and 4° C. by a factor of 2-50 over the control.

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All publications, databases, GenBank sequences, patents and patent applications cited in this Specification are herein incorporated by reference as if each was specifically and individually indicated to be incorporated by reference. 

We claim:
 1. A nucleic acid molecule comprising: (a) the nucleotide sequence SEQ ID NO: 47; (b) the nucleotide sequence that is complementary to the nucleotide sequence of SEQ ID NO: 47; or (c) a nucleotide sequence encoding an amino acid sequence that is at least 90% identical to SEQ ID NO:
 110. 2. The nucleic acid molecule according to claim 1, wherein the nucleotide sequence encodes an amino acid sequence that is at least 95% identical to SEQ ID NO:
 110. 3. A vector construct comprising: (a) a first nucleic acid having a regulatory sequence that causes transcription and/or translation; and (b) a second nucleic acid having the nucleotide sequence according to claim 1, wherein the first and second nucleic acids are operably linked.
 4. The vector construct according to claim 3, wherein the first nucleic acid is SEQ ID NO:127 or SEQ ID NO:128.
 5. A host cell comprising a vector construct according to claim
 3. 6. A host cell comprising a nucleic acid molecule according to claim
 1. 7. The nucleic acid molecule according to claim 1, wherein the nucleotide sequence encodes an amino acid sequence that is 100% identical to SEQ ID NO:
 110. 